The first half was a physical arm wrestle with both sides held scoreless for the first 29 minutes.
The Crusaders broke through for their opening try from Quinten Strange on the half hour mark with plenty of power and work from CodieTaylor in the set-up.
The first chance for points for the Blues came from the boot of Beauden Barrett who slotted a penalty.
With points hard to come by, the home side took the three as Richie Mo'unga converted a penalty before the half-time break.
The Crusaders held a narrow 10-3 lead heading into the changing sheds.
The home side pounced at the start of the second with Leicester Fainga'anuku scoring a blinder in the corner.
Blues captain Dalton Papalii was then handed a yellow card, later upgraded to a red, for a reckless late high tackle on Mo'unga.
The Blues were back to 15 men in the 63rd minute with just over a quarter of an hour to play and 12 points the difference.
Crusaders captain Scott Barrett said the Crusaders won the match with relentless defence.
"I think the game was won on our defence. To hold them to three points is a huge testament," Barrett said.
"At times it was probably a little bit ugly and we didn't fire too many shots.
"We closed down their game and a lot of their firepower didn't get into the game.
"It's huge, over the last couple of years the Blues have led the way in the round robin and it was a fierce game here."
Blues lock Sam Darry headlined the injury list. He came off second best in a crunching tackle, later to leave left the field with his arm in a sling.