The first Bristol derby in seven years ended in chaos after City beat Rovers in the Johnstone’s Paint Trophy.
Mounted police had to clear the pitch after City fans ran out of the stands following the 2-1 first round win at Ashton Gate.
Three Avon and Somerset Police officers needed treatment for minor injuries, with 12 supporters arrested after the pitch invasion.
In addition to the scenes after the match, there were several disturbances in the stands, with riot police needed to separate fans.
Chief Superintendent Caroline Peters said: "The majority of fans were well behaved and enjoyed the match.
"However there was a small minority who came with the sole intention of trying to spoil the enjoyment for the majority.
"We warned before the match that we would not tolerate any form of anti-social behaviour or violence.
"We will now aim to bring the offenders to justice using CCTV coverage and other intelligence and information gathered tonight to bring the offenders to justice."
City manager Sean O'Driscoll said afterwards: "It was great up until the final whistle. The scenes at the end are disgraceful."
"It took the shine off a good victory for us and that is what people will be talking about rather than the game itself.
"We didn't want what happened to happen and the players are disappointed as well.
"The game was played in a good spirit. It was competitive, but not over-zealous and we wanted the supporters to react in the same manner. Unfortunately, they did not."
The clubs had managed to avoid each other for so long after City became a Championship club, although they were relegated in the summer.
That means they entered the pot for the Johnstone’s Paint Trophy, a cup competition for League One and League Two sides, although neither side would have expected to face each other at the first possibly opportunity.