Gordon went down in the first half of the NSW Waratahs' 31-25 loss to the Western Force on Saturday after taking a quick tap and falling after 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.
On Monday, the Waratahs confirmed that he had undergone a successful surgery on a torn Achilles.
"The scrumhalf will be sidelined for a significant period and will miss the Wallabies' upcoming Nations Championship campaign," the statement said.
Gordon's absence is a fresh blow for the side as they prepare for the Nations Championship kicking off on July 4 and next year's home World Cup.
It will also add fuel to the fire on who will become Australia's first-choice No.9 with Tate McDermott only returning from a long-term hamstring injury in May.
ACT Brumbies playmaker Ryan Lonergan and Queensland Reds Kalani Thomas also loom as options.
Retired Wallaby James Slipper threw his support behind Gordon after hearing the news.
"I texted him the other day once I heard the news, so it's extremely disappointing for Jake," Slipper told AAP.
"He's a big cog in the Wallabies team ... he'll be sorely missed. It's one of those injuries that you don't want to see anyone get.
"One thing I do know is that he'll come back stronger from that so we're all behind him."
Waratahs coach Dan McKellar said after the Force game that he was "shattered" for the scrumhalf.
"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 is about to begin - disappointing," McKellar said.
