It was Chagaev's first defeat of his professional career in 27 fights and, with a heavy cut above his left eye, he was unable to come out for the start of the tenth round as the referee called a halt to the fight.
"You have seen the real world champion here tonight, thank you for your support," Klitschko told the 60,000-strong crowd with brother Vitali, the WBC champion, in his corner.
Only the WBA belt held by Nikolai Valuev eludes the brothers from Kiev.
"For me Chagaev is the best fighter in this weight division behind my brother and I, but I was better tonight," said Wladimir.
"This is the first time he has lost and he is a very good fighter.
"Every punch in this fight was important. Now I want to fight for the WBA belt and I promise you I will be back here again."
This was Klitschko's 53rd win to retain both his world titles against hepatitis B sufferer Chagaev, who was forced to call off last month's WBA title decider against Valuev in Finland because of medical concerns.
The 33-year-old Wladimir had also been scheduled to meet David Haye before a back injury ruled out the British fighter and Chagaev stepped in.
"Today wasn't my day, today belonged to Wladimir," said Chagaev.
"Throughout the fight I looked for the keys to unlock the win, but I just could not find them."
As the only fighter to beat Russian giant Valuev in April 2007, Chagaev, 30, spent most of last year out of the ring with an achilles tendon injury before he returned with an unconvincing win over Carl Davis Drumond last February.
Klitschko opened the fight by working his left jab with a low guard and kept his powerful right for the later rounds with his orthodox stance against the southpaw.
Chagaev was knocked down in the second round when Klitschko caught him with a straight right which stunned the Uzbeki who sat back on the canvas.
In both the fourth and fifth rounds, Klitschko dealt the challenger telling blows to the head and Chagaev responded with a low shot which scored against him.
The Uzbeki was a little slow in coming out for the sixth round and by the seventh a cut opened over his left eye.
Despite blood flowing down his face, Chagaev produced his best boxing in the eighth round with a spirited flurry, but the champion always had him at arms-length.
At the end of the ninth round the crowd at the Veltins Arena, home of Bundesliga football side Schalke 04, were on their feet as Klitschko landed several blows to the face.
The ring doctor went to his corner to check on the challenger's cut and the referee waved for the fight to be halted as the tenth round began.
Klitschko has an impressive 47 knock-outs from 53 wins fights.
The last of his three defeats as far back as 2004 against Lamon Brewster in Las Vegas when he lost the WBO title he later regained against Sultan Ibragimov in Madison Square Garden, New York, last year.
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