The goal came in extra time of Birmingham's second-round match at Yeovil to help resolve a fair play dispute.
Birmingham, the 2011 League Cup winners, had been leading 2-1 in the 90th minute before Byron Webster scored in stoppage time to take the match into extra-time.
It all started when Birmingham goalkeeper Colin Doyle kicked the ball out of play following an injury to a teammate. By convention, Yeovil would have sent the throw-in back to the visitors.
Instead, with defender Dan Burn still down and referee Darren Sheldrake allowing play to continue, Yeovil defender Webster quickly received the ball from the throw-in and kicked it into an empty net.
Birmingham was incensed at Webster's decision not to give the ball back, sparking ugly scenes between both sets of players before the match entered extra time locked at 2-2.
Compounding Birmingham's fury, Luke Ayling put Yeovil in front 14 minutes into extra time.
But straight from the restart, the Yeovil home fans were stunned when their team bowed to the convention of sportsmanship by allowing Lee Novak to run the ball into the net completely unchallenged to make it 3-3.
Second-tier Birmingham only managed to secure what it saw as a rightful victory by winning the penalty shootout 3-2.
Despite the narrow win, Birmingham manager Lee Clark was considering lodging a formal complaint about Yeovil's conduct.
"I think something has got to be done," Clark said. "It's always easy to give a goal back when you're leading.
"We were winning going into injury time. I'm proud of my players, every single one of them. I said to them before the penalties that whatever happens, even if they missed or scored, they have done the club proud."
Yeovil manager Gary Johnson conceded he sparked the flashpoint by urging his team to play on and not return the ball from the throw-in.
"I apologized to Lee Clark ... because, on reflection, it was ungentlemanly," Johnson said. "However, we get a bit fed up of teams kicking it out for their own players here when we're trying to get a goal back.
"I wanted us to play on but I didn't expect the Birmingham side to stand still, and didn't expect Byron to hook a goal in. I think people should look at this. How many teams are going to kick the ball out for their own players in the last minute?"