The match was heading for a goalless draw until Holt fired a low shot through a crowd from Kyle Turner’s corner kick in the 85th minute to secure the Jags’ first win in five matches and ensure they leapfrogged their opponents in the table.
The defeat condemned Inverness to an 11th consecutive match without a victory which leaves them eight points behind leaders Arbroath and a point ahead of fifth-placed Raith Rovers having played a game more than both.
Thistle meanwhile have closed the gap to Arbroath to just six points with a game in hand and boss Ian McCall admitted his side are title contenders.
"I think any of the top five could win the league, and we’re in the top five,” he said.
Inverness manager Billy Dodds admitted the result was “gutting for the players”, adding: “They are giving me their workload and effort, it’s just not falling for them at both ends of the pitch.”
Saturday’s fixtures in the Championship see top of the table Arbroath looking to end a four-match winless run at home to relegation-threatened Dunfermline, while second-placed Kilmarnock host a Hamilton side unbeaten in their last five.
Raith Rovers, without a win in 10, will climb back into the top four if they can end that run against Ayr United at Stark’s Park.
Bottom of the table Queen of the South, meanwhile, will hope to build on their positive start under new manager Willie Gibson at home to Morton.