The brash British boxer used his superior quickness against the huge Russian, who came close to being knocked down for the first time in his 16-year pro career in the 12th and final round.
Haye, a former cruiserweight world champion, won his third heavyweight fight to improve to 23-1 with 21 KOs, despite giving up nearly 28 centimetres in height and nearly 44kgs to Valuev.
Haye won over the judges with two scores of 116-112, while a third called it 114-114.
Valuev's record dropped to 50-2 with 34KOs.
Hayes first defence of the WBA belt will be against John Ruiz, who earlier beat German Adnan Serin in the seventh round by TKO.
Haye tried to keep Valuev on the move and opened with a left to the Russian's chin and a powerful combo while Valuev struggled to catch Haye, finding him only with left jabs.
The Londoner, nicknamed "The Hayemaker," connected with big rights and lefts to Valuev's head to build up a points lead.
Valuev finally came alive from the fourth round, but in sixth Haye landed a right-left combo and two solid lefts.
Haye continued to make Valuev work while finding holes, including a strong right followed by a left to Valuevs face in the ninth and a big right in the 10th.
As if he needed it, Haye finished off convincing the judges in the 12th round by landing two left hooks which left Valuev wobbly.
Valuev stayed on his feet but Haye knew he was the winner, raising his arms late in the 12th.
