Messi’s 14th Champions League goal this season took him past Ruud van Nistelrooy’s tally in the 2002-03 campaign.
Ivica Olic also scored twice on Tuesday as Bayern repeated its2-0 first-leg victory over Marseille to advance 4-0 on aggregate.
Bayern will likely face Real Madrid in the semifinals, with the Spanish leaders protecting a 3-0 lead over Cypriot team APOEL Nicosia on Wednesday. Chelsea will play Barcelona in the last four if the London club can defend a 1-0 lead over Benfica.
At the Nou Camp Messi put Barcelona one up after 11 minutes after being brought down in the penalty area by Luca Antonini.
But AC Milan always looked threatening on the counter-attack and they silenced the Nou Camp crowd in the 32nd minute when Antonio Nocerino scored after a good pass from Zlatan Ibrahimovic.
But Milan’s hope for an upset ended when referee Björn Kuipers awarded a penalty late in the first half when Alessandro Nesta was alleged to have hauled Sergio Busquets down. It was a soft call. The type of tussle we see on corner kicks across Europe every game. As Inter Milan, Arsenal and Real Madrid will all attest too, Barcelona gets the soft, nee dubious calls, at home in the big games.
Messi stepped up to score from the spot, his 14th European Cup goal of the season and it was always going to be difficult for Milan to comeback from that. When Iniesta scored in the 53rd minute to make it 3-1, Barcelona were heading to the semi-fianals for the fifth successive year
Bayern Munich is into the last four for the second time in the three years thanks in part to Bayern coach Jupp Heynckes resting Mario Gomez in favor of Olic.
And on a rare start, Olic delivered.
His first goal was an easy tap-in into the net in the 13th after former Marseille player Franck Ribery glided past the visiting defense to set up the Croatian.
Ribery also helped to create the second by feeding David Alaba down the left flank, and the Austrian midfielder crossed for Olic to nip ahead of his marker and score from close range.