The omission speaks to the prolonged slump in US relations with Pakistan that clouded a North Atlantic Treaty Organisation (NATO) summit where nations were eyeing the exits in Afghanistan.
Mr Obama readily acknowledged that the tensions raise questions about whether Pakistan will help or hurt the goal of a stable Afghanistan. Continued mistrust between the United States and Pakistan also threaten cooperation to eliminate Al Qaeda sanctuaries and could undermine US confidence in the security of Pakistan's growing nuclear arsenal.
"We need to work through some of the tensions that have inevitably arisen after 10 years of our military presence in that region," Mr Obama said Monday. "I don't want to paper over real challenges there."
Pakistan is not a NATO member but was invited to the summit on Sunday and Monday because of its influence in next-door Afghanistan and its role until last year as the major supply route to landlocked NATO forces there. Pakistan closed those routes after a US attack on the Pakistani side of the border killed 24 Pakistani soldiers in November.
The last-minute invitation from NATO to join the Chicago talks was a sign of hope that the rift had healed.
But it hasn't. And Mr Obama's dealings with Pakistani President Asif Ali Zardari made that clear on Monday.
Mr Zardari came to the US President's home town expecting a separate meeting with the US leader like the one accorded to Afghan President Hamid Karzai. But without a final deal to reopen the supply lines, no such meeting was to occur.
Mr Obama, along with Mr Karzai, did speak briefly with Mr Zardari on the sidelines of a large group meeting Monday. Mr Karzai dismissed the encounter in an interview with CNN as a "three-way photograph taking ... just a photo opportunity."
That was after Zardari had to sit by as Mr Obama opened Monday's session with public thanks only to the nations north of Afghanistan who allowed expanded supply shipments to transit their territory to compensate for the closed Pakistani border gates.
"I want to welcome the presence of President Karzai, as well as officials from central Asia and Russia - nations that have an important perspective and that continue to provide critical transit for ISAF supplies," President Obama said, referring to the International Security Assistance Force that is fighting the war.
Pakistani officials played down the snub.
"The supply route on Pakistan's side has been suspended for the last six months," Mr Zardari's spokesman Farhatullah Babar told reporters. "There was really no expectation from our side that the US president would appreciate and admire the suspension of the NATO supply lines."
The border crossing dispute is stuck over how much the US will pay Pakistan to allow trucks to transit its territory. Before the airstrike, the US paid about $250 per truck. Now, two US officials said, Pakistan wants $5,000 a truck and an apology for the deaths in the airstrike. The Obama administration has said it was willing to pay as much as $500 per vehicle and has expressed condolences and regret, but no apology. The officials spoke on condition of anonymity because the negotiations were being conducted in private.
The prospects for reaching a deal were unclear, even as the stakes grow larger.
Mr Babar said the government had asked negotiators to expedite an agreement, but that "no timeline can be given."
Mr Obama told reporters at the close of the summit that he knew beforehand that there would be no deal on the supply routes now.
"President Zardari shared with me his belief that these issues can get worked through," Mr Obama said. "We're actually making diligent progress on it."
President Zardari also met with US Secretary of State Hillary Rodham Clinton on Sunday and made a beeline across a meeting hall to grasp her hand again on Monday morning. The State Department said Mrs Clinton and Mr Zardari "discussed the importance of reopening the NATO supply lines," and of cooperating to fight terrorist threats.
The US and Pakistan have a history of troubled relations that started well before the terrorist attacks of Sept. 11, 2001. The road has grown only rockier since then. Pakistan has received billions of dollars in aid from the US over the past decade, but anti-Americanism is widespread in the country. And after years of sometimes meaningful cooperation in hunting down Al Qaeda figures, Pakistan is still seen by many US officials as double-dealing and unreliable.
The transit route issue was a distraction and an embarrassment for the United States at the summit, and Mr Obama's cool arm's length treatment of Mr Zardari made it look even worse for the Pakistani president.
"Pakistan has to be part of the solution in Afghanistan, and it is in our national interests to see a Pakistan that is democratic, that is prosperous and that is stable," Mr Obama said.
The quarrel over supply routes is intertwined with several other disputes, including Pakistan's opposition to US drone strikes against terrorist targets inside its borders.
In addition to closing the border crossings in response to the November attack, Pakistan ordered the US to vacate Shamsi air base, which the US was using to launch drone strikes at Al Qaeda and Taliban militants.
The top allied commander in Afghanistan, Marine General John Allen, has tried to cast the supply route problem in the best possible light, while acknowledging that he'd like to see the border crossings reopened as soon as possible. General Allen said Sunday that by some measure, war stocks are higher now than when the crossings were closed.
That is thanks to an increased - and much more costly - use of alternative routes, including a network of northern routes that connect Baltic and Caspian Sea ports with Afghanistan through Russia and Central Asia and the Caucasus. And they combine sea, rail and truck transport and are more costly than crossing Pakistan by land.
US officials have offered a range of estimates on how much the closing of the Pakistani land routes have added to the overall supply costs, but it apparently is at least two or three times more expensive to move supplies by air and via the northern route.
To underline the value of those alternative supply routes from the north, Defense Secretary Leon Panetta met on Monday in Chicago with his counterparts from the central Asian nations of Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan. He expressed his "deep appreciation for their support" of the northern supply route, Pentagon press secretary George Little said.
At least as troublesome as being forced to use alternative supply routes into Afghanistan is the issue of how to get war materiel out of the country as General Allen begins the withdrawal of thousands of US troops this summer. That's because the withdrawal includes shipment of vehicles and other equipment that would be costly and time consuming to remove by air.
The NATO alliance needs Pakistan's cooperation to ensure Afghanistan's long-term stability and security, NATO's top officer told reporters. That was a mild way of saying that Pakistan can play the spoiler at will and holds cards the fighting force does not. Pakistan shares history, culture and language with Afghanistan's restive southern swath, and maintains support for Taliban-led insurgents who cross the border to kill US and NATO forces.
