Mo'unga slotted four penalties and provided a deft chip kick over the defensive line that led to Bryn Hall's first half try in a stop-start match that never really got any flow on.
Blues counterpart Harry Plummer kicked two penalties for the visitors, who struggled in the set piece and did not threaten the Crusaders' line until Rieko Ioane crossed in the 71st minute.
The Crusaders moved to 53 points with the victory, 13 ahead of the second-placed Hurricanes, who have a bye this week
The Christchurch-based side have two games remaining and are all but guaranteed to finish top, with the Hurricanes needing to win all three of their remaining games with bonus points and hope the Crusaders fail to add to their tally.
It was a disjointed match in slippery conditions with the home side having had an unsettled preparation, having returned from South Africa late on Monday.
The nine-times champions were also accused of incidents of unsocial behaviour over the last fortnight while in Cape Town, with the team and New Zealand Rugby launching an investigation into the allegations.
Crusaders captain Sam Whitelock told Sky Sport it's been a challenging week.
"A few of the boys had a bit of lack of sleep this week, but things like that is why we play rugby, those challenges," Whitelock said.
Aided by his powerful forward pack, five-eighth Mo'unga slotted two early penalties then provided a deft chip kick over the defence, with Ryan Crotty gathering the ball and feeding the ball to Hall who scored their only try.
Plummer got the Blues going with a 23rd-minute penalty but neither side were able to trouble the scoreboard again with the Crusaders taking a 13-3 lead into halftime.
Mo'unga had a potential try ruled out when he dropped the ball over the line in a shoulder-high tackle by Melani Nanai, with referee Mike Fraser deciding the fullback had not stopped the playmaker illegally.
The decision incensed Whitelock, who argued with Fraser his side should have been awarded a penalty try.
Plummer added his second penalty to reduce the deficit to 13-6, although that was only short-lived with Mo'unga slotting his third less than two minutes later.
Ioane made the final 10 minutes tense for the home fans when he crossed to reduce the scoreline to 16-11, but Mo'unga kicked his fourth penalty to ease those concerns.