Austin carried on after several minutes of treatment and put Rangers ahead with a header from Matt Phillips' 40th-minute cross.
But 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 shot.
"Charlie's got a problem with his shoulder and we don't yet know the extent of it," said 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 crossbar.
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 added: "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."
- Sports & Recreation
- Matt Phillips