A Jon Toral brace in the first half made it a mountain to climb for a lacklustre home side, but a Yakou Meite goal and Lucas Joao saved penalty meant it could have been a very different result.
For Queens Park Rangers it was four matches without a win as they drew 1-1 with Millwall at the Den on Tuesday.
Midfielder Luke Amos is out until the New Year for Mark Warburton's side.
For play-off chasing Reading, both Joao and Meite picked up injuries in midweek and are looking like doubts for Saturday.
Queens Park Rangers:
Dieng; Kakay, Dickie, Barbet, Hamalainen; Ball, Cameron, Carroll; Osayi-Samuel, Bonne, Chair.
Rafael; Holmes, Morrison, Moore, Richards; Rinomhota, Laurent; Olise, Semedo, Ejaria; Baldock.
Ones to watch
With young star Eberechi Eze leaving the Hoops in the summer, his goals needed replacing.
Although there is yet to be someone as consistent as the current Crystal Palace midfielder, Ilias Chair and Lyndon Dykes are both popping up with crucial goals.
Each have five to their name so far this season.
For Reading, Joao remains the key player, although his missed penalty in midweek is the first sign that he is only human and will have off-days.
Academy graduate Michael Olise is also picking up plenty of plaudits this season, with eight goal contributions, and is attracting plenty of suitors for the coming couple of transfer windows.
Last season QPR failed to beat Mark Bowen's side.
Bowen's second game in charge was a midweek battle at the Kyian Prince Foundation Stadium and it finished 2-2, with George Puscas and Sam Baldock twice levelling after goals from Nakhi Wells and Jordan Hugil.
The Madejski match-up was a 1-0 home win on Boxing Day, and was settled by a John Swift long-range piledriver.
"They've started off really well, shown a really good attacking threat.
"They've got interesting data, very low possession, not many chances but ruthless, very clinical.
"They're a strong squad so we know what we face."
Meanwhile Serbian Paunovic is determined to return to winning ways in West London on Saturday, and prove just how good his side is.
"We've got to prepare the guys in the best possible manner, recover, replenish and get ready for QPR.
"We have to keep believing in what we have shown so far - playing good football, getting the ball on the ground and looking to affect the game in the final third with our creativity, our talent and our ideas.
"I want my team to be mature, to absorb the mistakes we make and the disappointment of defeat, and then come back and win the game. I want my team to come back when we are down.
"So we have one day to celebrate or cry over a result. Then the next morning, you have to lift your spirit, heal your wounds, stay positive and believe.
"Because we have shown everyone we can be a hell of a good team."
How to Watch
The game is not selected for television, so is available exclusively on iFollow.