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 final round.
"The key was my speed," Haye said. "People don't realize I am very fast. And I have a powerful punch. I'm athletic and if I wasn't a boxer I would be playing football or rugby."
Haye, a former cruiserweight world champion, won his third heavyweight fight to improve to 23-1 with 21 KOs, despite giving up nearly a foot (28 centimeters) and nearly 100 pounds (44 kilograms) to the tallest and heaviest champion in history.
"Everybody thought I was crazy. But I knew I could make him miss," Haye said.
Haye won over the judges with two scores of 116-112, while a third called it 114-114.
His first defense of the WBA belt will be against former titleholder John Ruiz, who earlier beat German Adnan Serin in the seventh round by TKO.
"He's a good fighter who is very underrated," Haye said of Ruiz. "He is not the most spectacular, but I don't feel like I will struggle with him. He's about the same size as me and I think I will knock him out."
Valuev's record dropped to 50-2 with 34 KOs, and he admitted Haye was too quick.
"Tonight only one thing happened that I didn't expect," Valuev said. "It was like a marathon for me. It was like a track event. I wasn't ready to run that much.
"The judges made their scoring and I think the last round made the difference, especially the end of it."
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.
Haye said he injured his right hand hitting Valuev in the head, most likely in the second round.
"It was like punching a brick wall," Haye said.
Nicknamed "The Hayemaker," he 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 the 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 Valuev's face in the ninth and a big right in the 10th. He wrapped up the fight by landing two left hooks that left Valuev wobbly in the 12th.
