The Ukrainian, whose lighter and smaller opponent took him the full 12 rounds despite fighting with a broken toe, was declared the winner 117-109, 118-108 and 116-110 by the two American and one South African judges.
While denied the 50th career knockout he had hoped for, Klitschko (56-3) had more than enough reason to celebrate with his brother and WBC champion Vitali.
They now hold the WBA, WBC, WBO, IBF and IBO belts between them and have achieved their lifelong dream of uniting the division in the family.
"I would have loved to celebrate my 50th knockout," said the youngest of the brothers, at 35, who was taunted publicly by the trash-talking English showman Haye in the build-up to the fight and had promised to punish him.
"I am still not OK with his behaviour before the fight," added the giant "Dr Steelhammer".
"It's definitely disgraceful to the boxing fans, to the sport of boxing, the way the man behaved himself. I think the fight talked for itself.
"He connected a couple of punches, I wasn't hurt in any situation in the fight," added Klitschko, who said Haye had been more cautious than any of the Ukrainian's previous opponents that the Briton had criticised.
"We have accomplished our dream and unified all of the best belts in the heavy division. I would call us now undisputed heavyweight champions," he said.
Klitschko aimed and landed far more blows than Haye, who was unable to connect with his famed "Hayemaker" while being picked off by his opponent's jab.
The 30-year-old Briton, now 25-2 after his first defeat in seven years, explained afterwards that had more to do with the secret injury he was carrying.
"I broke my toe about three weeks ago," Haye told Sky Sports television, baring his foot in the ring to prove his point. "I didn't let anyone know that.
"I've been giving it local anaesthetics in the gym ... that's why I stopped sparring. My Hayemaker wasn't there, I couldn't push off my right foot to land that shot. It was really frustrating."
Haye said he had considered pulling out of the fight but had refused to let down the considerable British support among the 50,000 strong crowd who made the trip to Germany for their biggest heavyweight fight in nearly a decade.
"There was no way after all the good fans had paid so much money to come over here, I could not pull out," he said.
Haye had sauntered into the football stadium with England's three lions on his shirt, the Union Jack on his shorts and a knowing grin on his face after keeping the restless crowd waiting for 10 minutes.
Singing along to the tune of Ain't no stopping us now, and with former champion and compatriot Lennox Lewis in attendance, Haye was jostled by the crowd as he forced his way to the ring but oozed confidence while his opponent remained stone-faced.
Yet, after all the hype, he could not deliver on a rainy night in Hamburg.
Klitschko, heavier and with a longer reach, dictated the early rounds and used his weight and height to push Haye to the floor repeatedly.
Genaro Rodriguez, the American referee, docked him a point in the seventh round for the offence but then controversially gave Haye a standing count in the 11th after what had looked like another blatant push.
Haye, who had vowed to "make the robot malfunction", kept his gloves contemptuously low for much of the fight and drew blood from Klitschko's right nostril in the fourth-round before himself suffering a cut to the nose in the fifth.
The Briton's punches were too often wild and off target while Klitschko used his left hook and jab to good effect.
"He's 30-odd pounds heavier than me and hit me with some of his best shots," said Haye, who reserved judgement on whether he will retire as stated in October.
"I didn't go down, I wasn't hurt at any stage. I think I've proved that I'm a great fighter," he said.
"He played it smart and kept hitting me with the jab and occasional right hand, all credit to Wladimir.
"He's a great fighter and I've got a lot of respect for him. Everything that was said in the lead up was for him to come and get me, so I had more chances of landing my shots."
Haye's manager and trainer Adam Booth said he had no argument with the outcome, only with the referee.
"I'm disgusted with the referee," he said. "Absolutely disgusted. Counted him [Haye] when he got pushed to the canvas instead of saying something ... I let my feelings [be] known to him at the end."