The Waratahs ended their two match losing streak when they beat the Rebels by 28 points to 9 in Sydney.
The loss was the Melbourne Rebels third loss in a row and takes their record to seven losses from ten matches.
The Rebels were a much improved unit compared to when the team's met in the first round and the Rebels lost 0-43 at home in Melbourne.
Bad weather prevented the game from being a free flowing affair with the Waratahs outscoring their opponents by three tries to none but two of the Waratahs tries came in the final 10 minutes.
Despite the 19-point win, the Waratahs struggled to subdue a Melbourne side who were gallant in defence but very limited in attack, with the match in the balance until the last 10 minutes.
The Waratahs, who thrashed the Rebels 43-0 in Melbourne's first ever Super 15 match in round one, had all the possession in the opening stages as they looked to press home their superiority.
They were held out by some resolute Melbourne defence, but the Rebels finally cracked after 12 minutes when hooker Tatafu Polota-Nau crashed over for the opening try.
The Rebels replied with two Julian Huxley penalties before Kurtley Beale made it 10-6 when Rebels scrum half Nick Phipps was penalised for shoulder charging opposite number Luke Burgess.
The match was played in wet conditions with periods of heavy rain, and both sides were unable to make any impression, the Waratahs heading into the halftime break slightly on top.
Huxley gave the Rebels the perfect start to the second period with his third penalty after just two minutes, but Beale restored the four-point advantage when the Rebels were penalised for slowing the ball down close to the line.
Beale kicked his third penalty moments later, giving the home side a handy seven-point break.
Then with the clock winding down the Waratahs finally put the game beyond doubt when lock David Dennis slid over following a bruising driving maul.
Mumm then scored in the last minute to rub salt into the Rebels' wounds.
Final Score Waratahs 28 Rebels 9
Tries - T. Polota-Nau, D Dennis, D Mumm
Pen - K Beale 3
Con - K Beale 2
Pen - J Huxley 3
Referees: Jonathan Kaplan (South Africa)
Assistant referees: Stuart Dickinson (Australia), James Leckie (Australia)
Television match official: Matt Goddard (Australia)
Waratahs :Kurtley Beale, Lachie Turner, Ryan Cross, Tom Carter, Berrick Barnes, Soseni Anesi, Luke Burgess, Ben Mowen, Pat McCutcheon, Dave Dennis, Sitaleki Timani, Dean Mumm (capt), Sekope Kepu, Tatafu Polota-Nau, Benn Robinson.
Replacements: John Ulugia, Al Baxter, Kane Douglas, Chris Alcock, Brendan McKibbin, Daniel Halangahu, Tom Kingston.
Melbourne Rebels:1 Rodney Blake,2 Ged Robinson,3 Greg Somerville,4 Alister Campbell,5 Hugh Pyle,6 Jarrod Saffy,7 Michael Lipman,8 Gareth Delve (vc),9 Nick Phipps,10 James Hilgendorf,11 Peter Betham,12 Stirling Mortlock (c),13 Mark Gerrard,14 Lachlan Mitchell,15 Julian Huxley
16 Heath Tessmann,17 Laurie Weeks,18 Hoani Macdonald,19 Tim Davidson,20 Richard Kingi,21 Cooper Vuna,22 Danny Cipriani