The former Reading and Leicester defender struck early on in Saturday's Championship clash, and Bolton captain Kevin Davies hit a second just before the break to give the home side some breathing space. Watford fought back in the second half and Lloyd Doyley's cross-cum shot provided a tense finish for both sides.
Bolton went close after only two minutes but Manuel Almunia made a great save from Marcos Alonso's header and the ball was cleared off the line.
Gianfranco Zola's side didn't heed the warning though and were behind a minute later. A Chris Eagles corner was well met by Mills and despite Almunia getting a hand to it, he could not keep it out.
Watford's first sight of goal came 10 minutes later but after moving infield, Mark Yeates dragged his shot, which was easily held by Adam Bogdan.
Owen Coyle's side went close to another as the first half wore on, but Almunia was quick off the line to stifle an David Ngog shot. The striker was well into the action and just a minute later spared his side's blushes by clearing a Nyron Nosworthy header off the line from a Watford corner.
Bolton's Eagles continued to cause problems from set pieces, this time swinging in a dangerous cross that Davies could only head over but with three minutes to go to half-time, Bolton doubled their lead and once again, a ball into the box from Eagles did the damage, with Davies steering the cross into the far corner.
Yeates almost grabbed a goal back out of nothing before the break, but his speculative volley from the edge of the area cannoned back off the crossbar and Jay Spearing hooked the ball clear.
The first chance of the second half came after 50 minutes. Ngog crossed to Davies but the ball was only half cleared into the path of Eagles and his rasping goalbound shot was diverted wide by Nosworthy, but Watford looked dangerous too, and a Daniel Pudil 20-yard drive went just wide of Bogdan's far post.
Watford were rewarded for their impressive start just before the hour mark after Doyley's cross eluded Bogdan and found the far corner, and the away side continued to press with Nosworthy going close again with a header from a Yeates corner but the defender could not hit the target.
Kevin Davies had a really good chance to calm the home supporters' nerves with 12 minutes to go after substitute Benik Afobe picked him out, but the Bolton captain could only head straight at Almunia, though Bolton were able to hang on for the points.