Kessler knocked the wind out of his opponent's sails in the second round with a right to the body that left Magee visibly struggling and the Northern Irishman was given a standing eight count after turning his back following another punch to the stomach later in the round.
It was a matter of when, not if, the relentless Dane would stop the contest and Magee's bravery was ended with yet another body shot, forcing referee Luis Pabon to call a halt to proceedings after 24 seconds of round three.
Magee became the WBA's regular champion after Ward was promoted to super champion at 168lbs although he was a firm underdog after agreeing to go into Kessler's back yard.
Following a rather uneventful opening round, Kessler brought the crowd to their feet with a straight right to the body midway through the second that sent Magee to his knees.
The 37-year-old managed to beat the count and valiantly looked to take the attack to Kessler, who focused all of his attack to the waist of Magee.
He was in pain towards the end of the round and took a knee after turning his back following another body shot.
Magee was saved by the bell, but the minute recovery in between rounds was clearly not enough and his resistance was ended when Kessler sent yet another straight right to the weakened area to bring a premature end to the night.
Kessler's routine win has already set tongues wagging about a potential rematch with IBF champion Carl Froch, who has made no secret of his desire for another bout with the 33-year-old after being beaten by a close points decision when the two met in April 2010 in a pulsating encounter.
Froch was a guest pundit for Sky Sports 1 on Saturday and admitted the fighters' promoters have already been in discussions about a return bout next year, possibly in the United Kingdom.
"I think (a rematch) is already step one completed because they've had a productive conversation and it's looking promising that the fight can definitely happen in the spring or early summer in 2013," he said.
"They'll be talking now in the couple of days following that.
"The only sensible fight out there for the fans, for the television, for me and for Mikkel is the rematch.
"The first fight was a humdinger. Everybody loved it who watched it and to get the rematch everyone's going to get excited."
The two are friends and Froch, who defeated veteran Magee in 2006, claimed he was the one to tell Kessler to focus his attack to the body.
"I said to him 'if it's a quiet opening then have a look to his body'," added the self-styled Cobra.
"Well done Mikkel, you took my advice well but if you come to the UK you'll be leaving that black belt with me."