Leading 13-0 at half-time, the Crusaders never allowed the Blues within striking distance in the second half, denying the home side any real chance of coming back into the contest.
The Crusaders were the first to create scoring opportunities, with two close calls in the Blues' right hand corner.
Richie Mo'unga opened the scoring for the visitors with a tidy drop goal while the referee played a penalty advantage.
Handling errors from both sides ensued, as a combination of weather and final nerves made for scrappy rugby.
Mo'unga extended the lead with a cleanly struck penalty in the 30th minute to take the score to 6-0.
Former Blues halfback Bryn hall scored a snappy try from close range on the stroke of half-time to give the Crusaders a 13-0 lead at the break.
The second half began in similar fashion to the first, with the Crusaders finding themselves in the Blues 22 for extended periods of time.
They were rewarded for their efforts when another Mo'unga penalty took the score to 16-0.
The sold-out Auckland crowd finally had a reason to cheer in the 59th minute, when All Blacks halfback Finlay Christie pounced on a loose ball close to the line and dived over for the Blues only try.
Momentum seemed to be with the Blues, as they began to run the ball and make some breaks through the Crusaders line.
Time began to become an issue for the Blues, as scrum resets chewed up valuable minutes. They entered the final 10 minutes trailing 16-7 and needing a fast finish to pull off an unlikely win.
Sevu Reece made sure of things for the Crusaders in the 76th minute, latching onto an awkward grubber kick from Pablo Matera and scoring a try to end the Blues faint hopes.
Crusaders captain Same Whitelock was proud of his sides defence, which proved the difference in wet conditions.
"It's not all about scoring points sometimes, it's about stopping them from scoring," said Whitelock.
"We had to show effort tonight, that's something we've always talked about, and tonight the effort was great."
Blues captain Beauden Barrett was a frustrated figure after the game, rueing his side's slow start.
"We didn't fire a shot in the first half and we knew we needed to come up with some solutions," said Barrett.
"We had no option but to come out and throw everything at it in the second half.
"We've got to give credit to the Crusaders, their defense was fantastic. It's a tough one to swallow."
The win is the Crusaders 11th Super Rugby title, and ends the Blues winning streak at 15 matches.