It was a deserved reward for the Rebels who were the much better side but looked for a time like they would again fall short.
However the hosts continued to play with conviction and courage to knock over the perennial champions.
Two tries to halfback Nick Phipps, who had his best game of the season, as well as Mortlock's effort in the 69th minute, set up the victory at AAMI Park.
Mortlock's try came after the veteran centre, in only his second match this season, intercepted a pass and then charged to the line.
Knowing he would be caught short he off-loaded to his winger Cooper Vuna, who managed to spin in the tackle and again find Mortlock who touched down to the delight of his teammates who raced to congratulate their leader.
The Rebels trailed 19-10 at halftime despite dominating possession and territory, with the classy Crusaders, who were ranked second in the New Zealand conference, managing to find the points when they needed them.
The Crusaders finished with only one try for the match through lock Sam Whitelock in the 30th minute.
Superboot Tom Taylor kept his team in the match with a perfect record of four penalties and one conversion in the first half but his side didn't manage to add to that tally.
The visitors could rue their decision to start All Blacks Israel Dagg, Ben Franks and Kieran Read on the bench.
Watched in the stands by Wallabies coach Robbie Deans, Melbourne's Kurtley Beale delivered his second successive starring performance to continue to push his claims to wear the No.10 jersey in next month's Tests.
He tired in the second half but his teammates stepped up with Phipps, Vuna and Mark Gerrard among the best in the backs while locks Hugh Pyle and Cadeyrn Neville worked tirelessly.
Phipps' tries came in each half, the first in the 12th minute after he ducked through a gap from the back of the ruck to plant the ball.
His second came when he followed a Gerrard break and that gave his side a 23-19 lead with Beale adding the extras.
In a further blow for the Crusaders, backrower Read left the field appearing to nurse a sore back after he fell heavily in a lineout.
MELBOURNE REBELS 28 (Nick Phipps 2, Stirling Mortlock tries Kurtley Beale 2 cons 3 pens) bt CRUSADERS 19 (Sam Whitelock try Tom Taylor con 4 pens) at AAMI Park. Referee: Jaco Peyper.