Birmingham goalkeeper Neil Etheridge complained of being racially abused by spectators after his side forced their FA Cup tie with Blackburn to a replay.
Reda Khadra gave Blues an early lead, with Bradley Dack then levelling before Joe Rankin-Costello put Rovers 2-1 up.
Substitute James sent the tie to a replay, but his goal was overshadowed by the ugly incident.
Angry scenes quickly replaced those of jubilation when 18-year-old James scored, with Etheridge going to referee Keith Stroud on the halfway line to complain about comments directed at him.
Blues boss John Eustace said the club were dealing with the complaint and said they will "make sure Neil is OK".
"Neil was racially abused at the end, which is bang out of order," Eustace told BBC Radio WM. "There is no room at all in society, let alone football, for that."
A statement from Birmingham after the game said they will assist the Football Association and the authorities after the incident was included in the official's report.
Blackburn said they would also investigate, adding that the allegation had been "taken extremely seriously".
"The club has a zero-tolerance policy for all forms of abuse and discrimination, and will take the strongest possible action against any individuals identified for committing such offences," a Rovers statement said.external-link
The alleged incident and flare-up that followed on the pitch marred a hugely entertaining tie between the two Championship sides that now heads to St Andrew's to be settled.
Blues, whose only win in seven games now was against Forest Green in the third round, capitalised on a poor Blackburn pass in defence to take an early lead.
Khadra's skidding third-minute shot proved too much for Thomas Kaminski to keep out.
The Germany Under-21 international - who is on loan from Brighton, having spent last season at Rovers - went close to a second soon after but his shot squirmed underneath Kaminski only to bobble beyond the far post.
Ben Brereton Diaz twice tested Etheridge either side of that near miss from Khadra in a first half that produced numerous opportunities for both sides.
While Etheridge was able to push a Rankin-Costello shot on to the woodwork, Dack was there to tap in as the rebound bounced into his path.
Kaminski ensured the hosts remained level at the break, keeping out a diving header from Lukas Jutkiewicz in the final minute of the first half, but Rovers took the lead immediately after the break.
Just as they squandered possession in defence to concede the opening goal, Blues did the same after the restart to allow Rankin-Costello to find the bottom corner with the outside of his boot.
Jutkiewicz headed over and Khadra called Kaminski into action again as Blues searched for a leveller, while Brereton Diaz sent a big chance wide and Dack also failed to make the most of promising opportunity.
The home side were made to rue those misses as James met a pass from Hannibal Mejbri to coolly slot home from 12 yards.
