Brazilian champions Palmeiras were losing 2-0 at half-time but scored three goals in the second half to almost guarantee their place in the knock-out stage of the competition.
However, television pictures showed Penarol players attacking Palmeiras goalkeeper Fernando Prass and combative midfielder Felipe Melo after the final whistle.
The outspoken Melo had accused some Penarol players of racist abuse when they met in Sao Paulo and later warned he would not shirk from slapping his opponents in the face when they meet again.
He responded with punches as a mass brawl ensued on Wednesday.
"It's lamentable," said a clearly agitated Baptista. "Premeditated the way it was it could have been much worse.
"When we tried to leave the field the tunnel was closed and security guards stopped us from leaving. Our own security got us off the field and stopped something worse happening."
Palmeiras lead Group 5 with 10 points from four games. Penarol are bottom with three.
(Reporting by Andrew Downie; editing by Sudipto Ganguly)
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