Mickael Antoine-Curier looked to have scored a hotly-disputed winner for the visitors, the on-loan Dundee striker's 65th-minute goal infuriating the home players and fans, who were admant he was offside.
United twice hit the woodwork late on bfore Garry Kenneth's 93rd-minute header spared Craig Levein's men back-to-back home defeats.
It was hard luck on Accies, who had looked set to hold on for what would have been a deserved first away win of the season.
United were forced to change half their outfield line-up for the game.
Injuries and suspeions meant recalls for Kenneth, Sean Dillon and David Robertson and first SPL starts for Jennison Myrie-Williams and short-term signing Mark Fotheringham.
Hamilton welcomed back key men Mark McLaughlin and Simon Mensing, while David Elebert made his first appearance for a month.
After three straight away games in all competitions, United were at home for the first time since their 1-0 defeat to Motherwell a month ago.
They were also up against their bogey side, who beat them twice in league and cup last term, as well as coming within seconds of a controversiawin at Tannadice.
The last thing United needed was another injury but they almost got two inside seven minutes.
A nasty-looking challenge by Elebert on Fotheringham after just 30 seconds left the Anorthosis Famagusta-bound midfielder writhing around on the deck, though he was not seriously hurt.
The same applied to goalkeeper Nicky Weaver, who collapsed in a heap in his own net after colliding with Richie Hastings from a wicked Marco Paixao corner.
At the other end, McLaughlin was booked for shirt-pulling before Morgaro Gomis' swerving 25-yard shot produced an uncomfortable-looking parry from Tomas Cerny.
Myrie-Williams should have hit the target when well placed 10 yards out but the summer signing blazed over.
Neither side was showing any real quality but there was plenty of commitment, with a number of hefty challenges fortunate to be punished by nothing more than a free-kick.
Antoine-Curier almost gave Hamilton an unpopula lead from Hastings' corner just before the half-hour mark but his goalbound header was blocked.
The remainder of the half was without incident until Paixao blasted over from 10 yards in the final minute.
Myrie-Williams' cross almost reached Robertson soon after the restart before Paixao's audacious 35-yard free-kick dipped onto the crossbar after Weaver had strayed too far off his line.
United boss Levein took less than nine minutes to bolster his attack with the introduction of David Goodwillie for Robertson.
Fotheringham was then carded for clattering into James Wesolowski.
Gomis picked up a needless booking in the 63rd minute for preventing a free-kick being taken and two minutes later Accies took a controversial lead.
Claiming offside, United stopped playing as James McArthur chipped a ball through to Antoine-Curier, who hesitated for a second before slotting past a bewildered Weaver to a chorus of boos.
A furious Kennet berated the assistant who had adjudged the forward onside.
Wesolowski was booked for kicking the ball away before going down injured minutes later.
Missing their best attacking players, including top scorer Danny Cadamarteri, it was hard to see how United were going to get themselves back in the game.
Levein threw on Dale Hilson for his debut in place of new Scotland cap Craig Conway.
And with time running out, Antoine-Curier came off for Flavio Paixao, while Andis Shala replaced Myrie-Williams.
United were desperately unlucky not to level with two minutes left when Damian Casalinuovo headed against the post and Darren Dods smashed his follow-up against the crossbar.
Fotheringham's drive was inches wide in stoppage-time before Casalinuovo's 93rd-minute cross was met by a brilliant running header from Kenneth.