Despite dominating territory and possession in the opening stanza, the visitors trailed by a point at the interval but reclaimed the lead through a Dave Harvey penalty on 53 minutes.
Daniel Halangahu answered with consecutive penalty goals before Force winger Samu Wara scored the match winner 14 minutes from time.
The hosts had a chance to steal victory after the siren but a trademark turnover from Force skipper David Pocock sealed his side's first victory of the campaign.
Force debutant Harvey scored 16 points, including a try, a conversion and three penalties, while Adam Ashley-Cooper and Tom Kingston were the try scorers for the home side.
The Waratahs were left to lament a controversial no-try ruling to deny Ashley-Cooper a five-pointer early in the second half.
However, Michael Foley's men had only themselves to blame after repeatedly kicking away possession, attracting a chorus of boos from the 14,673 fans on more than one occasion.
It is the third narrow loss of the campaign for the 'Tahs who have made their worst start to a Super Rugby season since 1998.
The Waratahs' decision to pass up an early penalty goal paid immediate dividends when Ashley-Cooper scored off the back of a rolling maul in the third minute.
Harvey opened the visitors' account with a penalty goal in the 10th minute, and when Waratahs lock Dean Mumm was yellow carded for not rolling away, momentum turned in the Force's favour.
Pocock opted for an attacking lineout rather than a 30m penalty attempt.
It proved the right call as flyhalf James Stannard took the ball to the line and delivered a one-armed pass to send Harvey over for his first Super Rugby try in the 18th minute.
The debutant converted to give the visitors their first lead of the night at 8-7.
The Waratahs spent most of the next 15 minutes defending grimly, but they hit the front when Kingston scored against the run of play three minutes from half-time.
Force half-back Brett Sheehan lost the ball in a tackle from opposite number Sarel Pretorius.
Pretorius kicked ahead for Kingston who regathered before turning on the jets to outsprint Alfie Mafi to the try line, with Halangahu converting from out wide for 14-11.
But the Force had the final say of the half when Harvey slotted a penalty goal after the siren to cut the deficit to one point at the break.
The Waratahs thought they had increased their lead when Ashley-Cooper crossed off a second-man play, however referee Jonathon White penalised Rob Horne for obstruction.
It proved a pivotal decision as the Force held on for a brave victory.