The Accies had not scored in their previous six league matches but took the lead after 17 minutes with a well-worked free-kick.
Alex Neil feigned to shoot but instead found James Gibson, who drilled the ball past Ryan Esson from the edge of the box.
Billy Reid's side looked to have claimed their third league win over Caley this season but Kerr popped up at the death to volley home and earn his side a vital point.
Inverness made one change to the side which lost at Aberdeen last weekend, with Latvian defender Pavels Mihadjuks (rib) missing out and replaced by Russell Duncan.
Accies also shuffled their pack, with Gibson replacing injured left-back Brian Easton, while Joel Thomas also started, with defender Chris Swailes dropping to the bench.
The match began in a fiery manner, with both sides determined to draw first blood.
James McArthur needed treatment following an early challenge with Ian Black.
Accies started brighter but struggled to create any opportunities from their early dominance.
However, Reid's side did open the scoring after 17 minutes with an inventive free-kick that came straight from the training ground.
Alex Neil feigned to shoot but instead slotted the ball into the path of Gibson, who drilled it low into the net beyond Esson.
The goalkeeper then had to be alert to gather a Gibson free-kick that deflected off the head of Richie Foran after 27 minutes as the visitors continued to press.
David Proctor surged forward from right-back to link up with Inverness team-mate Dougie Imrie but the defender's eventual shot was deflected wide.
Paul McGowan then should have doubled Hamilton's advantage when he went clean through but shot straight at Esson in the Caley goal.
Black, who had picked up the first booking of the day, fired wide after 38 minutes as the home side pushed for an equaliser.
Filipe Morais spurned a great opportunity as the half drew to a close when he failed to keep his lob over Tomas Cerny under the crossbar.
With manager Terry Butcher's words still ringing in their ears, it was the home side who took the game to their opponents after the break.
A Black free-kick fell to Morais but his effort was blocked after 50 minutes and the Portuguese attacker was denied by a fine Cerny save a minute later.
Butcher made his first change on the hour mark, replacing a midfielder with an additional striker, as Adam Rooney came on for Duncan.
Imrie should have grabbed an equaliser after 63 minutes but he headed wide following excellent work by Morais.
Hamilton, who were still looking dangerous on the counter, made a double substitution, with McGowan and Thomas making way for Kenny Deuchar and Derek Lyle.
The visitors were hanging on despite the relentless Caley pressure and Cerny breathed a huge sigh of relief when a looping header from Black fell just over the bar after 72 minutes.
Ross Tokely played as an auxiliary forward in the closing stages as Butcher's men fought to get something from the match with time running out.
With only eight minutes remaining, Hamilton made their final change, with Grant Evans replacing Simon Mensing.
However, with time running out, the visitors failed to properly clear a Foran cross and the ball fell kindly to Kerr, who volleyed home from the edge of the box to give his side a share of the spoils.
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