As well as getting him back on the goal trail the strike also ended Wolves own mini crisis that had seem them lose three of their previous four games.
But for Colchester it was an almost inevitable defeat. As so often happens it came in the first game after Williams had picked up the accolade of Manager of the Month for September.
Colchester had arrived at Molineux on the back of a six-match unbeaten run - all the more impressive considering they had lost their first four games of the season.
They created enough chances to have kept that unbeaten run going but were crucially found wanting in front of goal.
Bothroyd's decisive piece of finishing stood out when he nipped in front of two defenders six yards from goal to steer home a free-kick from Rohan Ricketts and seal a narrow but deserved win.
Once they fell behind, Colchester could still have saved themselves but Kemal Izzet saw his drive blocked and Jamie Cureton flashed a snap shot into the side-netting.
Colchester must then have sensed it would not be their day when Izzet saw his goalbound shot tipped around the post by Matt Murray.
A combination of poor finishing, the woodwork and one inspired piece of goalkeeping had ensured the first half ended goalless.
Jemal Johnson and Colchester's Karl Duguid were both guilty of squandering clear cut early chances, before Wolves were frustrated by the woodwork when Bothroyd slammed his 25 yard free-kick against the foot of the post.
But Colchester's Richard Garcia was most at fault in front of goal seven minutes before half-time when he sliced wide from eight yards after Pat Baldwin had flicked on Kevin Watson's corner.
It could have been a costly miss as Wolves were twice inches away from breaking the deadlock in the final five minutes of the half.
U's goalkeeper Aidan Davison fumbled a low drive from Ricketts and was relieved to see it roll just wide.
Davison made amends in stoppage time - pulling off a smart one-handed save to push away a powerful drive from Seyi Olofinjana.