Mo'unga also converted Andy Ellis' 61st minute try that had finally given the seven-times champions the lead after a resilient defensive effort from the home side had frustrated them for much of the match.
The Crusaders lead the competition on 45 points, three ahead of the Waikato Chiefs.
Todd Blackadder's side dominated possession and territory but were unable to break down the Blues defence, with one first half tackle from prop Charlie Faumuina on Johnny McNicholl so ferocious it knocked the Crusaders winger out of the game.
Fellow winger Nemani Nadolo, who returned following a four-week suspension, was at the heart of much of the Crusaders' early endeavour and opened the scoring with a try in the corner after some superb buildup work before his side spent a significant amount of time inside the Blues 22-metre area.
The Blues, however, refused to buckle and took what opportunities they had, with flyhalf Ihaia West scoring a try after they charged down a Crusaders clearing kick.
West and Mo'unga then traded penalties before Blues centre George Moala crashed over for a try that West converted to give the home side a surprise 15-10 lead at halftime.
The Blues defence again proved difficult to breach in the second half and they stopped two potential Crusaders tries when they prevented the attackers grounding the ball over the line.
Mo'unga and West again traded penalties to keep the gap at five points before Ellis finished off a midfield break from Kieron Fonotia to enable the Crusaders to draw level then take a 20-18 lead when Mo'unga converted.
Mo'unga then slotted the two late penalties that gave his side breathing room, which was needed when Piers Francis kicked a penalty for the Blues after the fulltime hooter had sounded.
Original source: Mo'unga kicks Crusaders to win over Blues