Championship Coventry were leading 1-0 and on the verge of dumping the 2008 winners out of the cup when captain Stephen Wright threw the visitors a lifeline with a 90th-minute own goal.
With penalties looming after a deadlocked extra time, Mokoena headed home to earn his side a 2-1 win and revive hopes of another lucrative Cup run for the Premier League's bottom club who next play Sunderland.
"It was very important that we won this game so we can build from it. We needed it badly," midfielder Mokoena told the BBC after his first goal for the club.
Birmingham City, the only other Premier League club in action, set up a fourth-round clash at last year's losing finalists Everton after ending Nottingham Forest's 18-match unbeaten run with a 1-0 win.
Birmingham also had a Cameron Jerome effort cleared off the line in the closing minutes of the third-round replay at St Andrew's.
