"I congratulate you for attracting a majority of votes … I hope you will prefer real public interests and justice to the endless demands of a selfish minority," Ahmadinejad told Obama in a statement published by IRNA.
Iranian officials have said Obama's election victory on Tuesday showed the American people's desire for fundamental change in domestic and foreign policy from the policies of President George W. Bush, who labeled Iran part of an "axis of evil."
"The great Iranian nation welcomes real, fundamental and fair changes in America's behavior and policies, particularly in the Middle East region," Ahmadinejad said.
Tehran and Washington cut diplomatic ties shortly after Iran's Islamic revolution, which toppled the U.S.-backed Shah.
The two countries have since been at odds over various issues, including Iran's nuclear program, which Washington and its European allies say is a cover to build nuclear bombs. Iran insists its aim is to generate electricity.
Washington has accused Iran of funding, equipping and training militants in Iraq. Iran denies this and says insecurity is due to the presence of U.S. troops who should quit Iraq.
Ahmadinejad said he hoped Obama would put an end to the United States' "war-oriented" policies.
"Other nations expect war-oriented policies, occupation, bullying … and imposing discriminatory policies on them to be replaced by those advocating respect … and non-interference in other countries' state matters," he said.
Obama has said he would toughen sanctions on Iran but has also held out the possibility of direct talks to resolve rows, including Tehran's nuclear dispute with the West.
The president-elect, like Bush, has not ruled out military action although he has criticized the outgoing administration for not pushing for more diplomacy and engagement with Iran.
Tehran has warned its response to any military action would be tough and would include targeting U.S. interests and America's ally Israel.
Iran's Prosecutor-General Ayatollah Qorban-Ali Dori- Najafabadi called on Obama on Thursday to show goodwill and remove sanctions against the Islamic Republic, the semi-official Mehr news agency reported.
"Through the lifting of the past government's cruel sanctions against Iran, Barack Obama can demonstrate his goodwill to the Iranian people," he said.
"Calling for forgiveness and remorse for the past U.S. government's deeds by the new government can bring about the great Iranian nation's forgiveness."
Iran's refusal to suspend its sensitive nuclear work has led to three rounds of U.N. sanctions since 2006, as well as bilateral punitive measures by Washington.
Iran has rejected world powers' demand to halt uranium enrichment, a process that can have civilian and military uses, in exchange for trade and other benefits.
(Reporting by Hashem Kalantari and Hossein Jasseb; Writing by Fredrik Dahl and Parisa Hafezi; editing by Caroline Drees)
