Pato opened the scoring for Milan in the 47th minute when he collected a cross from Robinho and beat Plzen goalkeeper Marek Cech.
The Brazilian pair switched roles a minute later and this time Robhino was the scorer.
Milan appeared to be heading for a comfortable win untl the final minute when David Bystron scored. Four minutes later Michal Duris scored the equaliser.
Plzen finished the group in third place behind Milan, with Barcelona on top and BATE Borisov in fourth place.
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