They also conceded the first try when Adam Ashley-Cooper ran around Robbie Fruean to put wing Atieli Pakalani over, but the Crusaders' big centre quickly made amends when scoring his own try from a set move and then setting up Zac Guildford for a five-pointer.
Fruean had an excellent game in the finish, also scoring a try in the second half when sneaking down the sideline following some Israel Dagg and Guildford magic.
There was some good stuff from the Crusaders and there was also a fair bit of dross.
The scrum wasn't as dominant as usual and the lineout only started to take off late in the second half when the Waratahs got their own jitters in this area.
The return of McCaw after 56 minutes is a real boost, though, and the intensity lifted following his arrival for blindside flanker George Whitelock.
The Highlanders' excellent come-from-behind win over the Cheetahs earlier in the day meant the Crusaders had to win to keep up with their southern rivals in the New Zealand conference.
Again the tactics appeared to be all about kicking the ball to the opposition and letting them make mistakes. Having seen it work so well against the Stormers and to a lesser extent the Hurricanes, it made sense to try it again, but the strategy only works if the kicks are executed well.
Too often the Crusaders appeared flat-footed when receiving the ball but gradually Fruean and Dagg worked their way into the game and both were welcome threats to a team which appeared to lack shape at times.
The Crusaders haven't lost to the Waratahs since 2004, a run of nine victories before kick-off and they looked to be doing just enough to lead 14-13 at halftime.
Tom Taylor, excellent with his goalkicking throughout with seven from eight, got them on the board straight after the break but Waratahs No8 Wycliff Palu scored an easy try to spark the Crusaders into action.
Adam Whitelock forced his way over thanks to an assist from Kieran Read. Taylor and Brendan McKibban swapped penalties and Fruean scored his second after 55 minutes to ease the Crusaders out to 34-23.
More penalties followed for both teams before Pretorius scored to set up a grandstand finish.
"We're really stoked to come away with the win there,'' said Crusaders skipper Read. "It was a really tough game, they brought it to us on attack there and never gave up. Full credit to our boys, we got stuck in there and were able to hold on in the end.''
Crusaders 37 (Robbie Fruean 2, Zac Guildford, Adam Whitelock tries; Tom Taylor 4 cons, 3 pens) bt Waratahs 33 (Atieli Pakalani, Wycliff Palu, Sarel Pretorius tries; Brendan McKibban 4 pens, 2 cons, Berrick Barnes con)
HT: 14-13