"With the concurrence of the chairman of the Joint Chiefs of Staff, I have recommended and the president has accepted and will nominate General David Petraeus as the new commander of the Central Command," he said.
General Raymond Odierno, until recently Petraeus's number two in Iraq, will be nominated to replace the general as the top commander in Iraq, he said.
Gates said he recommended Petraeus "because I'm absolutely confident that he is the best man for the job."
Noting that the United States faces asymmetric challenges in Iraq, Afghanistan and elsewhere in the region, Gates said: "I don't know anybody in the US military who is better qualified to lead in that area."
Petraeus will not leave his post in Iraq until late summer or early fall, and he will still make a recommendation in mid-September on whether a drawdown of US forces in Iraq can continue after the last surge brigade leaves in July, he said.
The long lead time, and Petraeus's replacement by his former right hand man were intended to avoid disrupting the momentum gained from the surge and to assure a smooth transition, Gates said.
"I am honored to be nominated for this position and to have an opportunity to continue to serve with America's soldiers, sailors, airmen, marines, coastguardsmen, and civilians," Petraeus said in a statement.
The Central Command post makes Petraeus responsible for US forces and operations in a broad swath of volatile territory that includes Afghanistan, Pakistan, Iran, Iraq and other hot spots in the greater Middle East.
The position opened last month after Admiral William Fallon abruptly resigned as Centcom commander following reports of differences with the White House over Iran.
Gates was asked whether Petraeus's nomination signaled a turn to a harder line on Iran than that taken by Fallon who had counseled diplomacy and patience in dealing with Tehran.
The secretary said he believed: "General Odierno and General Petraeus and Admiral Fallon were all in exactly the same position when it came to their views of Iranian interference inside Iraq.
"And it is a hard position because what the Iranians are doing was killing American servicemen, and inside Iraq. And so I don't think that there is any difference among them on that issue whatsoever," he said.
