The Waratahs were held scoreless in the second half by the Lions, but did enough before the break to win 29-12 at the Sydney Football Stadium on Saturday.
The hosts crossed the whitewash five times in the first half to bag the all-important bonus point, and repeat of last year's hammering of the Lions looked to be on the cards.
But the Waratahs packed up shop in the second forty, and failed to post any more points after an impressive opening 36 minutes that ultimately proved sufficient in picking up their tenth consecutive win over the Lions.
The hosts got off to a great start in the second minute when Kurtley Beale put Lachie Turner away down the right wing with a crisp pass and backed up on the inside to touch down out wide.
But their Johannesburg-based opponents hit back just before the quarter-hour mark when full-back Jaco Taute was first to reach a grubber-kick from Butch James.
However, the Waratahs then took control as Sosene Anesi scored twice and Beale latched onto a crossfield kick from Berrick Barnes and then floated a pass over to Ryan Cross for the try.
To add further despair for the Lions, winger Deon van Rensburg was sin-binned for 10 minutes immediately after the try for an indiscretion in the build-up.
Replacement Tom Kingston also bagged a try and it was 29-5 at half-time, but the Waratahs were happy to sit on their lead after that and spent the second-half kicking the ball away.
The Lions were able to claim the only try of a dour 40 minutes when replacement Dylan Des Fountain crossed with 10 minutes left.
The win pushes the Waratahs back into the top six and keeps them mathematically in the hunt for pole position in the Australian conference ahead of their two-week trip to South Africa.
Tries: Beale, Anesi 2, Cross, Kingston
Cons: Kurtley Beale 2
Tries: Taute, Des Fountain
Waratahs: 15 Kurtley Beale, 14 Lachie Turner, 13 Ryan Cross, 12 Tom Carter, 11 Sosene Anesi, 10 Berrick Barnes, 9 Luke Burgess, 8 Ben Mowen, 7 Chris Alcock, 6 Dave Dennis, 5 Sitaleki Timani, 4 Dean Mumm (c), 3 Sekope Kepu, 2 Tatafu Polota-Nau, 1 Benn Robinson.
Replacements: 16 Damien Fitzpatrick, 17 Al Baxter, 18 Kane Douglas, 19 Hugh Perrett, 20 Brendan McKibbin, 21 Daniel Halangahu, 22 Tom Kingston.
Lions: 15 Jaco Taute, 14 Lionel Mapoe, 13 Alwyn Hollenbach, 12 Doppies la Grange (c), 11 Deon van Rensburg, 10 Butch James, 9 Jano Vermaak, 8 Joshua Strauss, 7 Michael Rhodes, 6 Derick Minnie, 5 Van der Merwe, 4 Wikus van Heerden, 3 Patric Cilliers, 2 Bandise Maku, 1 JC Janse van Rensburg.
Replacements: 16 Edgar Marutlulle, 17 Jacobie Adriaanse, 18 Warren Whiteley, 19 Cobus Grobbelaar, 20 Rory Kockott, 21 Elton Jantjies, 22 Dylan des Fountain.