Arsenal even had the luxury of again being over-elaborate around the box before Cesc Fabregas found the net with a shot from distance on 84 minutes.
Emmanuel Adebayor added a second in stoppage time.
Milan showed flashes of form but most of the team failed to shine with last May's win over Liverpool now a distant memory.
Filippo Inzaghi, who scored twice in that final, hardly got a kick against Arsenal's backline and the 34-year-old sums up the problems at San Siro.
Arsenal's average age was 24.5 while Milan's was 30.2.
Milan's much-hyped 18-year-old Brazilian Alexandre Pato had a game to forget while Arsenal won the midfield battle, snuffing out the threat from a lackluster Andrea Pirlo.
Kaka, returning from two games out with knee trouble, tried to hide Milan's distinct lack of pace with some darting runs and Paolo Maldini also played well in his last European game.
The 39-year-old retires at the end of the season and had dearly wished to finish his glorious career with a record ninth European Cup final and a sixth winner's medal.
It was not to be but the one-club man bows out with dignity.
"Arsenal won because they played better," he said.
Arsenal coach Arsene Wenger said his plan to use Fabregas and Mathieu Flamini to contain Kaka worked to perfection.
"We decided not to give him time on the ball and it turned out that we decided well," Wenger said.
Manchester United and Fenerbahce also advanced to the quarterfinals.
Cristiano Ronaldo scored his 30th goal of the season in all competitions to give United a 1-0 victory over Lyon at Old Trafford and advance 2-1 on aggregate.
"It's fantastic for a wide player to do that," United manager Alex Ferguson said. "Obviously he drifts into the middle at times as he did tonight. He's done very well and made a good contribution."
Fenerbahce beat Sevilla 3-2 in a penalty shootout after the teams finished 5-5 on aggregate. Sevilla won the match 3-2, but Fenerbahce had beaten the Spaniards by the same score two weeks ago.
Fenerbahce goalkeeper Volkan Demirel then made three saves in the shootout.
(Agencies via Shanghai Daily March 6, 2008)