Klitschko recovered from an unexpectedly shaky start to finish off his opponent with a straight right after softening him up with a flurry of punches, according to Reuters.The American, who just failed to make the count, had opened up a cut over the Hamburg-based Ukrainian`s eye in the second round of the scheduled 12-round bout.
However, from the sixth round on Klitschko increasingly took control, landing a series of powerful shots to Thompson`s head.
"He`s an incredible boxer, he was exactly as difficult as I expected," said Klitschko, 32 who has 51 wins and three defeats.
"He was in top form and went all out to win. It was a lot of fun to box against a fighter like him. He put me under a lot of pressure. But I never thought it would be as hard as it was."
His win was clearcut but hardly overwhelming although it was a better fight than his February 23 win in New York over Sultan Ibragimov of Russia which gave him the World Boxing Organization belt to add to his International Boxing Federation title.
On Saturday, there was one farcical moment when Thompson was tripped by Klitschko in the 10th round and both fighters hit the canvas with the American taking a while to walk off his injury before he was finished off in the 11th round.
Boxing in front of a home crowd of 12,000 and a television audience in 100 countries, Klitschko was far from impressive in the early rounds despite being the heavy favorite.
The man known as `Dr Steel Hammer` also looked slightly nervous after blood streamed across his face from a cut opened over his eye when the pair clashed heads in the second round.
But Klitschko grew stronger as the fight continued. He wore down his tiring opponent even though Thompson appeared able to absorb most of his punches until the final two rounds.
Despite outboxing Thompson through the second half of the match, Klitschko opted to keep pounding away from safe distance until the 11th when he sensed Thompson was finally fading.
The American, 36, wept in his corner after the defeat before recovering moments later to tell the sell-out crowd he never saw Klitschko`s knockout blow.
"He hit me with a perfect punch," said Thompson. "I couldn`t see it. I got up and thought I could keep going but we had a great referee and I respect his judgment."
Thompson, who suffered the second defeat in his 33rd professional fight, said Klitschko had foiled his strategy.
"Wladimir is a great champion," he said. "He was the better boxer. They put in a great game plan to stop the things I wanted to do. I could have executed better but I got tired for whatever reason. I had to change tactics and that played into his hands."