In slippery conditions that featured pouring rain at times at HBF Park, the Force trailed 20-7 after 30 minutes of Saturday night's match but scored the next three tries to snatch a 24-20 lead by the 61st minute.
In an epic finish, Apolosi Ranawai got the ball through a pack of players to put the Waratahs back in front in the 67th minute, before Carlo Tizzano scored what proved to be the match-winning try in the 71st.
But the big news of the night was on the injury front, and it was all bad news for both the Waratahs and Wallabies.
First, Pete Samu's knee twisted awkwardly in the ninth minute when he slipped on the wet turf while bracing for a tackle.
The powerful No.8 tried to play on through the pain, before eventually trudging to the bench, with the injury later revealed as a medial ligament issue.
But the biggest disaster arrived in the 39th minute when Gordon took a quick tap and went down after taking a couple of steps.
Gordon looked gutted and in extreme pain as he was assessed by a medico, before being carried off the field by two trainers.
"This is gut-wrenching ... poor Jake," former Wallabies scrumhalf Nic White said in commentary.
The Wallabies' Nations Championship kicks off on July 4, and the expected loss of Gordon is a big blow to Australia's No.9 stocks.
"I'm shattered for Jake," Waratahs coach Dan McKellar said.
"No one cares about New South Wales and the Waratahs more than Jake, and just for him to do it in the last game of the season before the Test season's about to begin - disappointing."
The Force's brave comeback means they finished the season in seventh spot with a 7-7 record, marking their best campaign since their 9-7 year in 2014.
The eighth-placed Waratahs (5-9) are set for some soul-searching after their star-studded squad fell well short of expectations.
"A really good note to end on," Force captain Jeremy Williams told Stan Sport after the match.
"It's awesome we could get the win and finish the season on a high. Although we haven't made it to finals, which was our goal, we've really developed over the last couple of years and I'm really proud of the effort."
The Force stole two line-outs in the space of a minute early in the match, but poor clearance kicks each time meant when the Waratahs finally won a line-out, they made the home side pay via a try to hooker Ione Moananu.
Dylan Pietsch scored the Force's first try in the 25th minute when he capitalised on a loose ball in the try zone after scrambling Waratahs flyer Harry Potter failed to touch it down.
Potter made up for his mistake a few minutes later when he found a gap to score, extending NSW's lead to 13 points.
A yellow card to Tahs inside centre Joey Walton in the 34th minute for a shoulder-to-the-head tackle proved costly.
A minute later, some fancy footwork from Zac Lomax was followed by some even fancier moves from Pietsch as the Force winger crossed for his second.
In an epic finish, Tizzano scored two tries either side of Ranawai's effort to twice thrust the Force into the lead - the second time for good.
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