Clarets boss Sean Dyche bemoaned a sloppy start as Burnley failed to recover from losing two goals in the first nine minutes against Reading.
The Royals inflicted Burnley’s first home defeat of the season as they climbed above the Clarets to third in the table with efforts from Nick Blackman and Lucas Piazon.
Tendayi Darikwa pulled one back in the second half with his first goal for the club, but Burnley suffered a first defeat in six games.
Dyche, who was unhappy with the failure to award a penalty for handball against Michael Hector from a Sam Vokes shopt, said: “It’s unusual for us to start so sloppy, they scored the first from us crossing the ball, a breakaway and a bit of a mix up, and the second was good play from them.
“After that the response was excellent, the chances we created were certainly enough to get something from the game, we kept them to mainly long distance, and I’d still like a decision to go our way, because I think the boy (Hector) has hand balled it when Vokesy’s blatted one.
“It’s not an excuse, but we’ve had a number of penalty decisions already not given.
“Generally, the performance was a good one, we moved the ball well, the tempo was good, the substitutes made a difference, and we probably should have eked something from the game, but it wasn’t to be.”
Dyche added: “I thought we were dominant after the goals, but they’re 2-0 up, they drop off and play on the counter, game management - they killed the game.
“They’ve done well with that, but we forged an excellent goal, and to get your right back knocking one in at the back door from a cross from the left is excellent.
“It shows the attacking intent we had, and the crowd clapped them off because they thought that’s a group who have given everything.”