The striker scored the game-breaking goal in the 77th minute and Cristiano Ronaldo finally killed off a resilient Royals outfit with United's second at the death.
"It was a difficult game," Rooney told MUTV. "You have to give Reading a lot of credit. They attacked us and it was an end-to-end game - probably the most difficult I've played in this season.
"But we got there in the end and we're delighted with the three points."
Rooney flicked home the opener well from Carlos Tevez's astute pass, but only after the England man had spurned several earlier chances at the Madejski Stadium.
"I had a few opportunities before the goal and maybe should have done better with them," he said. "It was a great ball by Carlos and I'm just delighted that I finished it."
Rooney revealed his frustration at the Dubious Goals Committee's recent decision not to credit him with the opener in the 2-2 draw at Arsenal in November.
"I've had one deflected goal and had it took off me, so maybe they need to look at the game a bit closer."