Song Billong made it 3-1 from close range after benefiting from a ricochet off Hyypia and then Aliadiere was controversially ruled onside before pulling back to Baptista, who slid into an empty net to cap a remarkable end to the half.
Eto'o also had a goal disallowed as he headed into the net from an offside position to cap a telling performance that was in stark contrast to that of Holland international Klass-Jan Huntelaar who made an inauspicious debut for Milan after leaving Real Madrid.