Nawaz Sharif, the apparent winner of Saturday's election, was in talks to form a new government in a stunning comeback for a former prime minister who was deposed in a 1999 coup and spent years in jail and exile.
Sharif has been less vocal against US drone strikes than his main rival Imran Khan, and is considered a pragmatist with whom Washington can work.
"My administration looks forward to continuing our cooperation with the Pakistani government that emerges from this election as equal partners in supporting a more stable, secure, and prosperous future for the people of Pakistan," Obama said in a statement.
He congratulated "the people of Pakistan on the successful completion of yesterday's parliamentary elections.
"The United States stands with all Pakistanis in welcoming this historic peaceful and transparent transfer of civilian power, which is a significant milestone in Pakistan's democratic progress," he said.
"By conducting competitive campaigns, freely exercising your democratic rights, and persevering despite intimidation by violent extremists, you have affirmed a commitment to democratic rule that will be critical to achieving peace and prosperity for all Pakistanis for years to come," he said.