Full-back Robbie Robinson, flanker Liam Messam and prop Sona Taumalolo, the Chiefs' top try-scorer this season, crossed to earn the hosts victory.
They failed to record a four-try bonus point, but the win still put them five points ahead of the Highlanders.
The majority of the Chiefs' players sported shaven heads in support of Shave for a Cure, organised by Leukaemia and Blood Cancer New Zealand.
But it was the Waratahs who caught the eye in the first 40 minutes as they dominated territory and possession only to trail 13-10 at the break.
They opened the scoring through young wing Tom Kingston, who burst through the midfield and managed to dot down despite the best efforts of Sonny Bill Williams, who almost held him up.
The Chiefs sprung back into action and replied in kind soon after through Robinson. A sweeping move up the field, with Aaron Cruden heavily involved, moved them close to the line and fittingly it was Cruden who threw the last pass to put Robinson in at the left-hand corner.
Cruden added a couple of penalties before the change of ends and Waratahs kicker Brendan McKibbin could only manage one, giving the Chiefs a lead they perhaps did not deserve.
But the home side were far and away the better team in the second half, dominating their opponents up front and making the dominance count out wide through one of the best back lines in the competition.
It did not take long into the second half for Taumalolo to again dot down, his fourth try of the season.
Williams, a constant threat in midfield, put an average kick through which bounced up kindly to Richard Kahui in his 50th Super Rugby appearance and he fed the number one to score.
Cruden added another penalty and when Messam crossed in the final quarter the game was up.
Openside flanker Sam Cane made an instant impact off the bench as he broke from a Waratahs scrum and intercepted, fed half-back Tawera Kerr-Barlow and he found a charging Messam for their third and final try.