Ponte fans in the 13,000 sell-out crowd tore down parts of the wire fencing and charged on to the pitch, with angry supporters surrounding goalkeeper Aranha.
Most of the other players ran from the field and, although the referee waited almost an hour in the hope of restarting the game, officials ruled that the players' safety could not be guaranteed and abandoned the match.
Police hit fans with batons and fired percussion grenades to subdue the crowd, said local news reports.
"I'd like to thank the true Ponte Preta fans that came, applauded and supported us but I can't condone the pitch invasion," said Ponte's president Vanderlei Pereira.
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"I know everybody was on edge, no one likes to get relegated like that, but there's no justification for vandalism."
The result means that with one game of the season left, Ponte Preta will be relegated to Serie B.
Ponte, who play in Campinas, a city of over one million people 60 miles from Sao Paulo, scored twice in the first 15 minutes then had a man sent off midway through the first half.
Vitoria came into the game in the second period with Andre Lima scoring after 57 minutes before Trellez grabbed a double, sending the home fans wild with rage.
The incident was the latest in a series of violent episodes to blight Brazilian football in recent years.
(Reporting by Andrew Downie; Editing by Ken Ferris)
