"I strongly condemn these unjust actions, and I join with the American people in mourning each and every innocent life that is lost," Mr. Obama said from the White House briefing room.
The president also brushed aside criticism from Republicans in Congress that his response hasn't been tough enough, saying that "they've got their constitutional duties, and I'm sure they will carry them out in the way that they think is appropriate. I'm president of the United States, and I'll carry out my duties as I think are appropriate."
Mr. Obama said Iran's accusations against the U.S. and other Western governments of meddling in their internal affairs were "patently false" and called the claims part of a "tired strategy" of scapegoating other nations.
"This is not about the United States and the West; this is about the people of Iran, and the future that they – and only they – will choose."
Mr. Obama said the protesters had shown a "timeless dignity" in demonstrating against what they perceived as illegitimate election results.
"Those who stand up for justice are always on the right side of history," he said.
President Obama also mentioned the now-famous video showing the death of 26-year-old Neda Agha-Soltan, who has become an icon of Iran's opposition movement.
"It's heartbreaking. And anybody who sees it knows that there is something fundamentally unjust about that."
CBS News White House correspondent Chip Reid asked Mr. Obama if comments from Senators John McCain (R-Ariz.) and Lindsey Graham (R-S.C.) that his response was "timid and weak" prompted him to take a more forceful tact today.
Mr. Obama said "all of us share a belief that we want justice to prevail" but he had weigh other presidential duties.
"I've got responsibilities in making certain that we are continually advancing our national security interests and that we are not used as a tool to be exploited by other countries."
When asked by Fox News correspondent Major Garrett "what took so long" to use stronger language, Mr. Obama insisted his stance has been consistent.
"As soon as violence broke out -- in fact, in anticipation of potential violence -- we were very clear in saying that violence was unacceptable, that that was not how governments operate with respect to their people."
"My role has been to say the United States is not going to be a foil for the Iranian government to try to blame what's happening on the streets of Tehran on the CIA or on the White House, that this is an issue that is led by and given voice to the frustrations of the Iranian people," the president continued.
At the center of the upheaval is Iran's disputed June 12 presidential election, which opposition supporters claim gave an illegitimate victory to President Mahmoud Ahmadinejad.
Supporters of reformist Mir Hossein Mousavi have since staged several demonstrations that have resulted in the deaths of at least 17 protesters at the hands of security forces.
On Tuesday, Iran's Guardian Council, the top electoral authority, said the results would not be annulled.
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