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.
Barry Ferguson broke the deadlock against the run of play with a left-footed shot in the 62nd minute, sending the in-form Premier League side through at the expense of their Championship visitors.
Birmingham also had a Cameron Jerome effort cleared off the line in the closing minutes of the third-round replay at St Andrew's.
Sheffield United earned a ticket to Premier League Bolton Wanderers after beating Championship rivals Queens Park Rangers 3-2 in a replay at Loftus Road featuring a flurry of three goals in the space of four second-half minutes.
Championship Derby County overcame League One Millwall 5-3 on penalties after their match ended 1-1 after extra time.
Cardiff and Bristol City must replay their all-Championship third-round tie after drawing 1-1 at a snowy Ashton Gate.
