An inside ball from Bernard Foley had Michael Hooper in open space and the flanker raced 30 metres before putting Ashley-Cooper over.
But two penalty goals each to Foley and Sharks centre Francois Steyn were the only additions to the scoreboard before the two sides broke for halftime.
There was more bad blood in the second half as Hoffman struggled to keep a lid on proceedings.
He was loudly jeered by Waratahs fans before overturning a dodgy call against the Tahs upon a video replay of Israel Folau's long clearing kick.
Cheika's mood didn't lighten when the Waratahs were caught napping after conceding a penalty in the 49th minute.
Rather than shoot for the line, Sharks five-eighth Lionel Cronje kicked crossfield for unmarked winger Odwa Ndungane, who swooped on the ball to stroll over untouched in the right-hand corner.
Steyn missed his sideline conversion attempt, leaving the Waratahs clinging to a two-point lead.
Waratahs fans - and Cheika - were on tenterhooks shortly after when TMO George Ayoub took several minutes to award blockbusting winger Taqele Naiyaravoro a try four minutes later.
At first look, Naiyaravoro appeared to lose possession but NSW's leading tryscorer in 2015 did well to retain control and ground the ball for his fifth five-pointer this campaign.
Foley added the extras, but the Waratahs' nine-point buffer only lasted two minutes before a converted try to Steyn reduced the margin to 20-18.
But two more Foley penalties, a late try to the five-eighth - and a dubious no-try ruling against Sharks winger JP Pietersen sealed victory for the Waratahs.
The end scoreline flattered the titleholders, who climbed back into the top six ahead of a 2014 final rematch next Saturday night with the Crusaders at ANZ Stadium.
Cheika admitted the scoreline didn't reflect the closeness of the match.
"We're just staying in there somehow. I'm not quite sure how," he said.
"I suppose we just expect such a high standard of play from ourselves, but tonight I think our effort was there.
"Perhaps we were even trying a bit too hard. They were so keen to get the ball moving again, get the movement back in our game."
Sharks coach Gary Gold said a sixth straight defeat was tough to swallow.
"We're a proud union and we're in uncharted territory. We haven't been this low on the log before," he said. "We just have to stay in the fight."