Both of Pompey's goals were heartbreaking for second-tier Coventry, coming in the last minute of normal time and in time added on at the end of the second half of extra-time.
The win gave Portsmouth fans a rare moment of celebration in an otherwise chaotic season, on and off the field, and Mokoena said it had come at a vital time for the south coast club.
"It was very important to win this game so we can build on it," Mokoena told ITV4. "We needed it so badly. It's a big win for us."
He added: "It's always difficult to come to these places and credit to Coventry, they made it difficult for us. At the end of the day we managed to wrap it up."
Portsmouth, the 2008 FA Cup winners, were behind for most of the match after Coventry striker Leon Best fired the home side into a 22nd minute lead.
And it seemed cash-strapped Portsmouth, whose officials met earlier Tuesday with Premier League chiefs in a bid to lift the club's transfer embargo, were about to exit the FA Cup until Coventry's Stephen Wright headed into his own net shortly before the end of normal time at the Ricoh Arena.
The tie was heading for a penalty shoot-out until defender Mokoena headed in the winner with virtually the last act of the game.
Scotland midfielder Ferguson struck from 15 yards shortly after the hour mark as Birmingham saw off in-form Championship high-flyers Forest and extended their unbeaten run in all competitions to 14 matches.
In Tuesday's only third round match Bristol City's late equaliser secured a 1-1 draw against Championship rivals Cardiff after substitute Gavin Williams scored in the second minute of stoppage-time at a blizzard-hit Ashton Gate to cancel out Michael Chopra's 76th minute opener for the visitors.
Wednesday's third round replays see Premier League Liverpool, looking to salvage a so-far disappointing season, at home to second-tier Reading while Championship leaders Newcastle face divisional strugglers Plymouth.
Source: AFP European Edition