The match had earlier been held up for five minutes when Rovers fans spilled on to the pitch to celebrate Peter Beadle's injury-time equaliser against the home side.
The Bristol City chairman, Scott Davidson, has launched an internal investigation but his club could now face serious sanctions. "We need to see the referee's report and what the police have to say," Steve Double, an FA spokesman, said. "But we're particularly concerned about reports that players were attacked."
Mounted police restored order after the initial pitch invasion but once the last few seconds of play remaining had been completed, a mob of City followers came on to the pitch and pursued Rovers players as they raced to the dressing- room.
At least one supporter was taken away on a stretcher. Chief Inspector David Harper, of Avon and Somerset police, said many arrests had been made inside and outside the ground. "There was certainly adequate stewarding and policing under normal circumstances."
Ian Holloway, the Bristol Rovers player-manager, blamed media hype for the trouble. "The build-up to this game locally was unreal and I was affected by it as much as anyone else.
"You end up with too much bickering and too much confrontation over what is just a game of football.
"Joe Jordan [the City manager] and I were able to have a drink together after the match, so why rival supporters can't do the same is beyond me.
"We had a great chance to show Bristol football in a good light. There was some good action, yet all we end up talking about is crowd trouble.
"I was worried for the safety of my players at the end, three of them made the mistake of leaving the pitch by the old tunnel and took some time getting back to the dressing-room.
"We had every right to celebrate our late goal and what followed was totally unacceptable.
Paul Agostino had given City a 16th-minute lead with a superb solo effort and the home side were in control until the 62nd-minute sending-off of Rob Edwards for chopping down Jason Harris, his second bookable offence. From then on Rovers sensed a reprieve and were helped when their crossbar denied Matt Hewlett and Kevin Nugent before Beadle, who had also struck the woodwork, proved to be their saviour.
Goals: Agostino (16) 1-0; Beadle 90 (1-1).
Bristol City: Naylor; Owers, Barnard, Edwards, Taylor, Hewlett, Goodridge (Carey, 63), Blackmore, Agostino (Goater, 68), Nugent, Tinnion. Substitutes not used: Kuhl.
Bristol Rovers: Collett; Pritchard, Martin, Browning, Clark (Skinner, 84), Tillson, Holloway, Hayfield (Cureton, 73), Harris, Lockwood (Archer, 63), Beadle.
Referee: D Orr (Iver, Bucks).
Bookings: City Barnard, Edwards, Carey. Sending-off: City Edwards, 62; Rovers Holloway.
Man of the match: Agostino.