The veteran Dutch midfielder felt that Bjorn Kuipers should not have penalized Alessandro Nesta for his alleged tug on Sergio Busquets shortly before the break at Camp Nou.
After last week's scoreless draw at San Siro, the Italian champion bowed out of Europe after suffering a 3-1 defeat, with the Blaugrana responding with a spot kick from Lionel Messi - his second of the game - and a strike from Andres Iniesta, after Antonio Nocerino's 32nd-minute leveler.
Milan was left enraged by Kuipers' handling of the game at Camp Nou, particularly in relation to the decision to penalize Alessandro Nesta for a tug on Sergio Busquets as the pair jostled for position ahead of a corner kick. But Seedorf tried to offer a considered analysis when he spoke to reporters after the game.
"The referee blew and the penalties were given," he mused. "It's true that I didn't see what happened but, speaking to the referee, for me he made a mistake [on the second penalty]. If he saw that a foul was being committed [before the ball was in play], he should have stopped the game, which is what always happens.
"That was a key moment in the game, but we didn't lose because of that. They were two important games between two important teams, and Barcelona had a little bit more. Let's leave it at that."
Seedorf believes that the Blaugrana will now go on to reach the final and is of the opinion that some familiar faces will be waiting for them at the Allianz Arena in Munich.
"The biggest contenders are Real Madrid and Barcelona," the former Madrid midfielder stated. "They are two very strong teams, but Bayern and Chelsea could put up a fight."
Meanwhile, Seedorf admitted that he had been touched by the reception he received from the home fans when he was replaced during the second half, confessing: "I am grateful to the Barcelona public for applauding me when I went off."
The 36-year-old Dutchman spent three seasons with Barca's great rival Madrid between 1996 and 1999.
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