The winner came three minutes from time when right-back Andy Griffin, making his home debut on loan from Stoke, slipped a ball into Gylfi Sigurdsson inside the penalty area.
The young Icelander cleverly turned past Kevin McDonald before shooting across Burnley keeper Brian Jensen into the far corner of the net.
It was no more than Reading deserved having had the better chances and being in control for the larger part of a relatively poor game.
It was the lowly Championship side who had all the early chances, three of them falling to lanky Polish striker Grzegorz Rasiak.
His first came after six minutes when Sigurdsson crossed from the left, but Rasiak tamely shot past Jensen's right-hand post.
Then Brynjar Gunnarsson sent Jobi McAnuff away down the right wing. The former Watford man did well to get a cross in, but it was a shade too high for Rasiak who headed over the bar.
Twelve minutes later there was yet another chance for Rasiak, but this time he had to take it quickly and again he sent it wide.
Rasiak took a tumble in the area after close attention from Tyrone Mears, but referee Andy D'Urso waved away claims for a penalty.
Burnley's first attempt at goal came two minutes into the seconds half, but Mears effort was far too high and caused keeper Adam Federici no problem.
Burnley's next effort came after 54 minutes when Graham Alexander lifted an effort wide of an upright. This sparked off Burnley's best spell of the game and Griffin did well to block a close-range effort from Chris Eagles.
There were strong claims for a Reading penalty 20 minutes from time when McAnuff was sent tumbling by Joey Gudjonsson, but again Mr D'Urso waived Reading's claims away. Skipper Ivar Ingimarsson was booked for leading the protests.
Federici had to make a full-length save from McDonald and when the corner came over he made a brilliant save from David Edgar and then watched as substitute Martin Paterson blazed over with the goal at his mercy.