Hill will oversee the withdrawal of US forces from Iraq by the end of 2011.
However, towards the end of George Bush's presidency, Hill was criticised for the way he handled the six-party talks on ending North Korea's nuclear programme.
Sam Brownback, a Republican senator, said that Hill had not considered Pyongyang's human rights record in negotiations and that he had drawn up a flawed agreement with North Korea.
"The deeds of ambassador Hill on North Korea: No progress on human rights, terrible deal, failed diplomacy," Brownback said in his final speech before the confirmation vote.
"The only thing dismantled in the six-party talks was our strategic deterrence and moral authority."
Detractors also say that he lacks experience in the Middle East and does not speak Arabic.
Hill's appointment was supported by General Ray Odierno, the commander of US forces in Iraq, General David Petraeus, the US commander of forces in the region, and Ryan Crocker, his predecessor, who left the post earlier this year.
Hill's brief will also include helping to undertake parliamentary elections, the passing of a long-awaited law on the sharing of oil revenues and aiding the nation's regional relations.