The Waratahs dominated the first 55 minutes to establish a 23-point lead then seemed to lower their intensity, allowing the Rebels to gain some momentum that was halted once Daniel Halangahu kicked a 70th minute penalty.
"The first 50 minutes everything went to plan and we executed well but getting involved in that niggly stuff let them back in the game," Halangahu said.
"It was really on out there and there was a lot of feeling... but I'm happy with the win."
Inside centre Tom Carter scored two tries and tighthead prop Sekope Kepu notched his first Super Rugby try for the Waratahs, while flyhalf Halangahu added two conversions and fullback Bernard Foley slotted a penalty.
Wallabies utility back James O'Connor, who moved to the Rebels in a controversial transfer from the Western Force at the end of last season, kicked two penalties in the first spell as the Waratahs went into the break with a handy 22-6 lead.
Foley secured the Waratahs bonus point when he crossed after another sustained build-up from the New South Wales side, who then seemed to switch off after establishing the 29-6 lead.
O'Connor added two more penalties and the Rebels forwards milked a penalty try, which also resulted in Waratahs' hooker Tatafu Polota-Nau being yellow carded, to make the scoreline closer than it should have been.
Halangahu, who had kicked an earlier second half penalty before the Rebels' try, slotted another with 10 minutes remaining to make the victory safe.
