From the striker's ensuing corner, Boateng produced a great first-time effort with the outside of his foot that went inches past Valdes' far post as Pazzini stood rooted.
El Shaarawy was then unlucky not to reach Boateng's floated ball in from the right on 36 minutes after Muntari had done well to win the ball in midfield.
No changes were made at half-time, but the game itself went on to change dramatically.
On 53 minutes tempers frayed when Sergio Busquets brought down Pazzini in midfield, earning the Spaniard a yellow card.
A Riccardo Montolivo free-kick from 30 metres bounced fortuitously off the hand of Cristian Zapata for Boateng, who beat Valdes with a superb strike from the edge of the area.
Barca protested but Scottish referee Craig Thomson responded by showing a yellow card to Gerard Pique.
Barcelona were showing little of the cohesion and possession football they had displayed in the first half while Milan, growing in confidence, were getting more bullish.
On 63 minutes, Barcelona replaced Cesc Fabregas with Alexis Sanchez but the change had little impact as Milan continued to frustrate the Catalans.
Muntari, unmarked on the left of the area, finished off some neat build-up play by El Shaarawy and M'Baye Niang to beat Valdes with a superb angled strike.
Barca rallied in the dying minutes and Carles Puyol came close with a header when he rose to meet a corner from the left, but they were unable to get what would have been a precious away goal and now face an uphill struggle to turn the tie around.
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