Obama also mounted a strident defense of American Muslims, paid tribute to believers who are fighting in US armed forces, and said Americans must remember who their true enemies were -- naming Al-Qaeda and "terrorists."
The president has vowed to forge a "new beginning" with Islam, but tensions have been sparked by a plan to build a Muslim cultural center near the felled World Trade Center in New York and a US pastor's threat to burn Korans.
"We have to make sure that we don't start turning on each other," Obama said at a White House news conference on the eve of the ninth anniversary of the September 11, 2001 attacks on the United States.
"And I will do everything that I can as long as I'm president of the United States to remind the American people that we are one nation under God and we may call that God different names, but we remain one nation.
"It is absolutely important now for the overwhelming majority of the American people to hang onto that thing that is best in us -- a belief in religious tolerance, a clarity about who our enemies are," Obama said.
"Our enemies are Al-Qaeda and their allies who are trying to kill us but have killed more Muslims than just about anybody on earth."
The president also reaffirmed the right for Muslim believers to build the cultural center, which includes a mosque near the "Ground Zero" site in New York, though said he understood the sensitivities.
"We are not at war against Islam. We are at war against terrorist organizations that have distorted Islam and falsely used the banner of Islam to engage in their destructive acts," Obama said.
"We have got to be clear about that. If we are going to successfully reduce the terrorist threat then we need all the allies we can get," Obama said, in a unequivocal, emotional statement at the end of the appearance.
Obama warmly praised former president George W. Bush, whom he regularly assails over the economy, for his efforts to ensure the 2001 attacks did not whip up a severe backlash against Muslim Americans.
And he branded a threat by Florida pastor Terry Jones to burn Korans on Saturday - which is now on hold - as "un-American" and warned people should not "play games" with US troops in war zones in Muslim countries.
"My hope is that this individual prays on it and refrains from doing it," Obama said, referencing his own Christian faith, and repeated his warning that such an act would be a recruiting tool for Al-Qaeda.