However, he was recalled against Bolton and took his chance by finding the target in the 56th minute.
It was only Nugent's third goal for Burnley but a welcome one at that and manager Owen Coyle has already indicated he would like to hold onto him.
Bolton made the breakthrough with a superb free-kick from Matt Taylor but were again unable to keep a clean sheet.
Steven Fletcher had a half chance for Burnley in the ninth minute but scooped his effort over the bar after Chris Eagles and Michael Duff had linked up.
Back came Bolton and Chris Basham tested Brian Jensen from distance with a powerful shot in the 14th minute.
Burnley then unsuccessfully appealed for a penalty after David Nugent went to ground following a tussle with Gary Cahill.
Referee Chris Foy would have none of it and waved play on to the annoyance of the home supporters.
Bolton launched a swift counter-attack and Kevin Davies tried to curl the ball beyond Jensen in the 21st minute.
It was a superb effort by the striker but finished marginally wide of the post.
Bolton kept up the pressure and a minute later Tamir Cohen thumped a shot into the goalkeeper's body from 25 yards.
Burnley should have taken the lead in the 24th minute after Wade Elliott won possession from Zat Knight. He squared the ball to Fletcher, who somehow found the wrong side of the post from six yards.
Bolton made the breakthrough in the 29th minute after Andre Bikey had been penalised for a challenge on Davies.
Taylor stepped up and delivered a magnificent free-kick from 20 yards that beat Jensen at his near post.
Burnley hit back and Eagles tried a snap-shot from 30 yards that goalkeeper Jussi Jaaskelainen took with a degree of comfort.
Ivan Klasnic almost added a second for Bolton in stoppage time after being set up by Taylor but Jensen parried his effort.
Burnley came close to equalising in the 50th minute when Kevin McDonald's shot beat Jaaskelainen only to bounce back off the underside of the bar.
However, Bolton should have extended their lead two minutes later when Davies flicked on a cross from Lee Chung-yong.
Taylor was the first to react but scuffed his shot wide of the post from close range.
Play switched back down the other end and Nugent carved out an opening for Fletcher.
However, the Scotland striker was again wasteful, blasting a shot high over the bar from inside the area.
Burnley, though, drew level in the 56th minute when Bolton failed to deal with Elliott's cross and Nugent headed home.
The home side stepped up the pace and Eagles cut inside but failed to test Jaaskelainen.
Then Fletcher got on the end of a cross from McDonald and showed good skill to work an opening, only to drag his effort wide.
Bolton were grateful to Jaaskelainen for making two point-blank saves from Eagles and Nugent in quick succession as they again found themselves on the back foot.
Nugent almost secured the points 10 minutes from time but he sent his effort across the face of goal and wide of the post.