Khamenei praised the large voter turnout at Friday's election, where President Mahmoud Ahmadinejad was re-elected with more than 62 percent of the vote, and said the result showed Iranians value "resistance against oppressors," the agency reported.
But clashes between police, supporters of the president and protesters opposing Ahmadinejad, dominated the capital Sunday.
Supporters of Mir Hossein Moussavi, an opposition candidate many analysts believed could unseat Ahmadinejad, allege the vote was rigged.
Hundreds of regular and riot police were on the streets as civil unrest continued for the second straight day.
But it was non-uniformed activists, on foot and on motorcycles, who appeared to be behind the most violent incidents.
Mahmoud Ahmadinejad, Iran's incumbent president, has defended his disputed re-election at a public rally in Tehran, insisting that the vote was not "distorted" as claimed by his rivals.
The speech was delivered amid reports of arrests of several reformist politicians who supported Mir Hossein Mousavi, Ahmadinejad's main challenger, and a formal appeal by Mousavi for the cancellation of Friday's vote.
Supporters of the conservative Ahmadinejad, waving Iranian flags and his portraits filled the capital's Vali Asr Street on Sunday to listen to his speech after the authorities declared that he had won a second four-year term by a huge margin over Mousavi.
What makes this interesting is the voter turnout which Mousavi supporters point out would have created millions of votes being counted within a few hours. They are claiming that the results were switched, appearing to believe that it was really Mousavi who had the over 62% majority.
Time is reporting the Iranian regime has cracked.
Even some of the most astute Iran-watchers are taken aback. "I don't think anyone anticipated this level of fraudulence,” says Karim Sadjadpour of the Carnegie Endowment for International Peace. “This was a selection, not an election. At least authoritarian regimes like Syria and Egypt have no democratic pretenses. In retrospect it appears this entire campaign was a show: Supreme Leader Ayatollah Ali Khamenei wasn't ever going to let Ahmadinejad lose."