Mo'unga was in the thick of everything the defending champions did well as they ran in seven tries to four against the belligerent South Africans.
The man who made his All Blacks debut in November after some sublime domestic form in 2017 was the game's influential figure.
He had a key hand in five tries, including scoring their last in a 15-point haul.
There will be some concern in the Crusaders' camp after Mo'unga's exit in the dying minutes after an apparent blow to the head.
Having helped his team power 26-0 ahead inside the opening quarter, Mo'unga's skill was called on again after the Stormers bounced back to trail only 31-21 with 25 minutes remaining.
The playmaker threw a slick pass to put winger Seta Tamanivalu over before dancing across himself to secure a second victory for the hosts after last week's 45-23 defeat of the Chiefs.
Missing a host of All Blacks, the Crusaders still had too much class, looking particularly dangerous out wide where slick inter-play prised open a fragile Stormers wide defence.
Winger George Bridge grabbed a first-half double but couldn't match his three tries from the equivalent match last year, which the Crusaders won 57-24.
Other tries went to hooker Codie Taylor, halfback Bryn Hall and flanker Billy Harmon in his first Crusaders start, replacing Matt Todd - out for six weeks with a broken thumb.
A romp appeared imminent before the Stormers sorted out their lineout and dominated possession through the middle stages.
All of the visitors' tries came through close-range charges by tight forwards. Props JC van Rensburg, Wilco Louw and Steven Kitshoff all crossed, along with lock JD Schickerling
The Crusaders are away next week to the Hurricanes, while the South African side, who have a 1-2 win-loss record, travel to Dunedin to face the Highlanders.