The bill passed on Friday night brings the amount spent by the US on the wars and other military operations to $507 billion since September 11, 2001.
Congress also passed other legislation dealing with national defence, internal security and illegal immigration.
The approval of extra funding comes before the mid-term elections to congress on November 7.
The senate approved the Pentagon budget by a 100-0 vote on Friday.
George Bush, the US president, signed the legislation the same day.
The bill provides $378 billion for core Pentagon programmes, an increase of about five per cent.
Wage increases for military
Legislation to convene military trials to prosecute terror suspects was also passed by the house.
However, a programme validating a warrantless wiretapping programme has been postponed until after the mid-term elections.
On Thursday, Republican and Democrat negotiators also agreed on a different defence bill which includes a 2.2 per cent pay rise for the military.
It also set policy on weapons spending and research programmes, considered vital to US national security.
The lower house passed the bill by a bipartisan 398-23 vote on Friday.