The striker's first-half header from a John Oster cross was the only breakthrough in a game of few chances and lifted the Royals into Premiership nosebleed territory.
Steve Coppell's side are now sixth after four straight league victories and leapfrogged Bolton into the European qualification places in the process.
Sam Allardyce named the same Wanderers side that had started against Chelsea in midweek, but it was the home side who started the brightest.
Steve Sidwell saw a side-foot effort dribble tamely wide from a Steve Hunt corner and James Harper's 20-yard drive drifted wide of the same post.
Bolton carved out a great chance to go in front on 15 minutes when Ibrahima Sonko went walkabout, allowing Kevin Davies to play captain Kevin Nolan into space down the middle. But Nolan's low shot was easily gathered by Reading keeper Marcus Hahnemann and the home side responded with their best passage of play.
Sidwell spooned a close-range effort against the crossbar, but his blushes were spared as Doyle was harshly ruled to have fouled Jussi Jaskelainen.
Then, from an Oster corner, centre back Ivar Ingimarsson found himself in a yard of space but side-footed wide without troubling the keeper.
But Reading's increasing dominance was handsomely rewarded on 33 minutes with a quite superb opening goal.
Left-back Nicky Shorey left Davies standing as he skipped inside the striker on the halfway line and clipped a clever cross-field ball to Oster on the right wing. The former Everton man carved Bolton open by stepping inside Stelios Giannakopoulos and clipping a clever lobbed cross to the far post where Doyle directed a header beyond Jaaskelainen.
It was a lead Reading fully deserved but Bolton nearly levelled just before half-time when El Hadji Diouf's toe-poke deflected off his own captain Nolan and wide.
The resulting corner - awarded incorrectly by referee Alan Wiley - was only half headed clear by Graeme Murty to present Nolan with a shooting opportunity but his drive from the edge of the box flew harmlessly wide.
Allardyce sent his mis-firing side out five minutes early during half-time but it hardly inspired a fight back.
In fact it was Reading who threatened early in the second half with Hunt's cross inviting Oster to volley only for the winger to blaze way over the bar.
Nolan did have a chance at the other end but dragged his shot wide after the ball had bounced kindly to him off Sonko.
But Reading continued to dictate and Shorey saw a curling effort dip just over after Hunt's persistence had set him up on the edge of the area.
Sidwell blazed over from a similar position after he was forced to rush his shot and substitute Leroy Lita forced a smart stop from Jaaskelainen after coming on to add pace late on.
But one goal was ultimately enough for Reading, despite some frantic late attacking from the visitors.