The Swede was incensed by referee Bjorn Kuipers' decision to award the Blaugrana their second penalty of the evening for a tug on Sergio Busquets by Rossoneri defender Alessandro Nesta, arguing that he should have had a spot-kick himself.
"How can he give a penalty like that?" Ibrahimovic told Mediaset. "If he gave that penalty, he should have given my penalty.
"The game is not about the man in green. It's a shame. I couldn't believe he called a penalty when the ball wasn't in play.
"It seems like Uefa wants a certain two teams in the Champions League final. Now I understand how Mourinho feels every time he comes to Camp Nou."
Messi had opened the scoring from the spot after being felled in the area by Luca Antonini but Milan had levelled the game and the tie through Antonio Nocerino, only to see the diminutive Argentine fire home for a second time from 12 yards out to restore the Blaugrana's advantage.
Andres Iniesta added a third goal for Barca after the break and the Catalans will now face either Chelsea or Benfica in the semis.
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