Obama telephoned Zardari, who was in Karachi, to discuss bilateral ties and the situation in the region, an official statement said.
The two leaders agreed to "take appropriate steps to repair the ties between the two countries on the basis of mutual respect and mutual benefit".
The US President appreciated Pakistan's efforts in the fight against militancy. Zardari said the fight against extremism was "Pakistan's own and it had to fight it to the finish in its own national interest".
The two leaders agreed to have "regular contacts and interaction at appropriate levels for the resolution of issues," the statement said.
Pakistan-US ties have been buffeted by several incidents this year, including the shooting and killing of two Pakistani men by CIA contractor Raymond Davis in January 27 and the US raid that killed al Qaeda leader bin Laden in the garrison city of Abbottabad on May 2.
Islamabad virtually cut off defence and intelligence cooperation in the wake of the raid against bin Laden and told Washington to cut the strength of American military personnel deployed in Pakistan.