Austin carried on after several minutes of treatment and put Rangers ahead with a header from Matt Phillips' 40th-minute cross.
Rangers' 15-goal striker eventually had to come off in the second half, by which time his team were 2-0 up courtesy of Karl Henry's 20-yard strike.
"Charlie's got a problem with his shoulder and we don't yet know the extent of it," explained QPR assistant boss Kevin Bond.
"He had to come off after going on as long as he could. In the end it was too much for him and we'll have to assess it.
"He's as game as they come and got his goal from a great cross by Matt Phillips.
"We know we're reliant on Charlie and didn't need reminding."
Bolton had gone close to opening the scoring when Craig Davies' powerful effort hit the bar.
They caused the hosts problems and pulled a goal back through Jay Spearing's 85th-minute shot from near the edge of the box, but were unable to find an equaliser.
Bond admitted: "We were in control of the game but got a bit sloppy in the last 10 minutes and conceded a goal.
"We made really hard work of it in the end and that was not very pleasing. I also didn't think we played very well for the first half an hour.
"Our tempo was too slow, both with and without the ball, and we needed to pick that up.
"We know we need help in the attacking area and will be working hard between now and Friday to bring someone in."
Bolton are struggling at the wrong end of the table and have won only one of their last eight league matches.
But Trotters boss Dougie Freedman insisted: "We've just got to keep going and things will change for us.
"I felt we were very unfortunate. The little things are just not going for us but the performance levels and the commitment are both there.
"We've got to make sure that we keep the standards high and on another day the shot that hit the bar goes in.
"I'm very proud of the lads' effort. We felt we were very unlucky not to take the lead on a few occasions and felt hard done by to be 1-0 down.
"In the second half we gave it a right good go and gave them a good run for their money, but QPR's experience and ruthlessness helped them.
"We played against a very good team and we weren't just defending. We broke on them and played some good stuff, especially in the first half."