Tries from wing Seta Tamanivalu, centre Jack Goodhue and number eight Kieran Read extended the Crusaders' record as the most successful team in the competition.
The Lions played for 41 minutes with 14 men following a red card for flanker Kwagga Smith.
The home side hit back with two tries in the final 15 minutes through hooker Malcolm Marx and prop Corne Fourie to add some life to the closing stages, but the Crusaders closed out the match.
They become the first side to cross the Indian Ocean to win the Super Rugby final. The Lions are still waiting for their first title, having now been losing finalists twice running.
There were guts from the home side, but no glory in what was the final match in charge for coach Johan Ackermann, who will join English side Gloucester this coming week.
(Reporting By Nick Said, editing by Neil Robinson)
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