The Trotters made most of the running in the first half but were undone when Austin headed home Matt Phillips' 40th-minute cross from the right.
And Henry doubled the lead five minutes after the break, firing into the bottom corner from 20 yards.
Jay Spearing pulled a goal back late on but Bolton, who have won only one of their last seven league matches, were unable to find an equaliser.
Second-placed Rangers' narrow win kept them in touch with leaders Leicester and was a major boost given their recent injury problems.
Without the sidelined Joey Barton in midfield, they also had to deploy on-loan Tottenham left-back Benoit Assou-Ekotto as a makeshift right-back because of injuries to Danny Simpson and Nedum Onuoha.
But their problems pale into insignificance compared to those of Wanderers, who are struggling near the wrong end of the table, were beaten 7-1 at Reading in their previous away game, and lost Tim Ream after the first challenge of the match.
Defender Ream was hurt in an accidental clash of heads with Austin only a few seconds after the opening whistle.
Nevertheless, the visitors made a strong start and after Mark Davies did well on the right and pulled the ball back for Darren Pratley, Assou-Ekotto had to react quickly to block the midfielder's shot.
Mark Davies and forward Craig Davies both then shot wide, and there was more anxiety among the home fans when Austin went down with what appeared to be a shoulder injury.
Rangers, heavily dependent on their top scorer this season, were relieved when Austin was able to continue after undergoing lengthy treatment.
And QPR survived another scare when Craig Davies' blistering 25-yard shot crashed against the bar with Rob Green well beaten.
They made the most of their good fortune, nicely working an opening for Austin to score his 15th goal of the season.
Henry's first goal for QPR then gave them even more breathing space, although Bolton remained a threat and Green had to produce two fine saves.
Shortly after the tipping over Lee Chung-yong's effort, the keeper dived to his right to push away Medo's powerful strike.
Rangers appealed in vain for a penalty when Andy Johnson went down under a challenge from keeper Andy Lonergan.
But they found clear-cut chances hard to come by and had to endure an anxious finish after Spearing's 85th-minute shot from just outside the area flashed past an unsighted Green.