A war of attrition between the competition's two best defensive teams was only decided in the closing stages through the boot of first five-eighth Daniel Carter.
Two tries to electric winger Lachlan Turner gave the Waratahs a 12-3 lead after 30 minutes but they were not to score again as the grinding dominance of the Crusaders forward pack eventually reaped its reward.
The home side scored only one try but All Blacks star Carter landed four penalties and a dropped goal for a decisive 15-point haul which complemented his astute kicking in general play.
Victory gave the masterful Deans his fifth Super title before he packs his bags on Monday to take up a four-year contract as the Australian national coach.
All smiles afterwards as he thanked the soldout crowd of 26,000 at AMI Stadium, Deans would have been shifting uneasily in his seat for much of the match as the Waratahs' defence stubbornly refused to crack.
A yellow card to Crusaders lock Brad Thorn midway through the second half would have produced the most jitters, with Deans' men having clawed their way to a 14-12 lead by that stage.
However, they kept the game scoreless for the next 10 minutes and clamped their control when the burly forward returned to the fray.
It was a remarkable seventh title for the Crusaders in their ninth final appearance.
The Crusaders employed a traditional finals football approach, using forward drives and high tactical kicks in the early stages and rugged mentality at the breakdown which forced several turnovers.
The Waratahs were also disciplined in their approach, with the occasional touch of magic from Kurtley Beale balanced by a clutch of mistakes from the teenage first five-eighth.
All Blacks captain Richie McCaw was at his inspirational best on the Crusaders openside flank, getting best support from hooker Ti'i Paulo and flanker Kieran Read while lock Ali Williams largely ruled the aerial dogfights.
Durable flanker Reuben Thorne came off the bench with three minutes remaining to become the only player to appear in all nine of the Crusaders' final appearances.
The Japan-bound Thorne was playing his last first-class game in New Zealand.
Waratahs loose forward Wycliff Palu was typically powerful with ball in hand while Turner and fellow wing Lote Tuqiri were the chief attacking threats but had few opportunities.
It was also the last game in charge for Waratahs coach Ewen McKenzie, whose contract was not renewed by the NSW Rugby Union midway through the competition.
Carter had the Crusaders 3-0 up in the fourth minute through a penalty after a collapsed scrum.
However, Turner grabbed his first try four minutes last off a pinpoint cross kick from Beale, plucking the ball from Carter's grasp on the right flank.
His next try in the 25th minute was brilliantly executed.
It began when Waratahs captain Phil Waugh intercepted a Carter pass, chugging 30m and setting up an overlap for Turner. He chipped the defence and sped past Crusaders halfback Andy Ellis to collect and score.
Carter, who had a mixed night with the boot, landed an angled penalty to begin the fightback process before No 8 Mose Tuiali'i crossed in the right-hand corner 2min before the break in an important psychological score.
While the Crusaders still trailed by one point at halftime, momentum had swung in their favour.
More pressure led to a Carter penalty and a lead they weren't to surrender although the Waratahs then enjoyed their best period of the game as they camped in Crusaders territory.
The game's most controversial moment came in the 56th minute when Crusaders prop Wyatt Crockett scored from a sweeping move but play was called back on a report from South African touch judge Cobus Wessels, who reported Thorn for throwing a punching back on the halfway line.
Reduced to 14 men the Crusaders closed the game down effectively and only pulled clear through a dropped goal and penalty to Carter.
The Crusaders nearly had their second try in the dying moments but winger Scott Hamilton spilled the ball with the line open.
There was a bizarre moment as the on-field celebrations began when a horse bolted loose on the field and galloped for several laps before being corralled.
McCaw was unperturbed, revelling in another victorious season and the end of an era at the franchise.
"There was a lot of emotion out there and I guess there will be more tonight," he told Sky Sport.
McCaw sensed his side were getting on top at halftime and that it was a matter of time before they hit the front.
"We had played a lot of the rugby. When you've got the ball and you're breathing pretty hard, well you hope that they are too, making all those tackles," he said, acknowledging his side stepped up to another level while Thorn was sidelined.
"At times like that you have to really dig deep. When you're down to 14 it sometimes hardens your resolve even more."
His opposite, Waugh, was magnanimous in defeat.
"They deserve to win the title, they won the round robin convincingly and we were outplayed tonight so good on them," he said.
"I said before game it was about 80 minutes and we just didn't go on with it after halftime.
"We didn't score a point in that second half ... the difference was probably the amount of pressure inside our own half."
