Watkins’ 10th minute strike allowed Inverness to leapfrog United into second place behind leaders Hamilton in the Scottish Premiership table.
The visitors started the game well and were unlucky not to take the lead when Chris Erskine’s effort struck a post but it was Caley who found the net when Watkins poked the ball home from close range to put Inverness in front.
United keeper Radoslaw Cierzniak had to be at his best with a smart fingertip save to prevent Watkins from grabbing his second goal of the game.
Caley defender Josh Meekings struck the post with an excellent effort while Gary Mackay-Steven also went close just before the break.
After the interval, Thistle’s Billy McKay raced clear but he could only manage to fire his shot straight at Cierzniak in the United goal.
James Vincent also had a chance to seal it when he was through on goal with only Cierzniak to beat, but he dragged his shot wide as he attempted to double Caley’s lead late on.