Referee Bjorn Kuipers pointed to the spot after the former Italy international had tangled with Blaugrana duo Carles Puyol and Sergio Busquets in the area as they awaited the delivery for a corner shortly before half-time.
Milan were incensed by the decision, given the ball had not been in play at the time, and Nesta has admitted that he has no idea why he was penalised.
"I pulled Puyol out of the way but only after he blocked me," the World Cup winner is quoted as saying by Milan's official website. "Not a single one of the players protested."
Despite the controversy caused by the penalty, which Lionel Messi converted to set Barca on their way to a 3-1 victory, Nesta conceded that the better side had progressed to the semi-finals.
"Barcelona are strong," the centre-half admitted. "If you leave them space, they start to play like they know how.
"There’s a big difference between us but I think that Milan have the economic power and the technical talent to get closer and one day or another this [Barca] team will start to fall.
"I think that in these two games we’ve shown that they can be beaten. But it’s true that they have Messi, who’s like having an extra player and good for them that they have him!
"We were unlucky and there's no shame in losing to the best in the world. I’m sure that Milan will react and that after a couple of years we’ll be back dreaming like we used to."
Nesta admitted, though, that he has probably played his last Champions League game for the Rossoneri, saying: "I’m going out with my head high because at 36 years of age, I gave all I could."
The former Lazio captain, who has been recently linked with a move to Juventus, has won two Champions League titles during his decade-long Milan career.
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