Steven Gerrard's brace of penalties and Luis Suarez's late effort condemned United to a sixth defeat on home soil this season in all competitions, leaving them way off the pace of the Premier League's top four with time to make up the ground rapidly running out.
Things could have been worse for United at Old Trafford with Gerrard missing a third penalty - which had seen Nemanja Vidic dismissed for a second yellow card - while right-back Rafael da Silva was lucky not to see red himself.
United rarely threatened throughout the contest as their woes under David Moyes continue and Rooney expressed his dejection after the final whistle.
"It's one of the worst days I've ever had in football," former Everton striker Rooney told MUTV.
"It's hard to take. You have to give Liverpool credit – they played well – but it's difficult to take. Nobody wants to lose, especially in this way, in your own stadium. It's not nice."
Gerrard's second came in the first minute after the interval and Rooney conceded the timing of the goal rocked United's confidence.
"To go behind by one penalty was hard to take," Rooney added. "We had a game plan for the second half, which went out the window when they got the second penalty so early on.
"It made it an uphill battle to come back. I thought after that we had a couple of chances where I thought, if we got one, we could have gone for a second and maybe we could have done it. Obviously it didn't happen, though.
"Then, to concede a third penalty, even though they missed, was a big blow to us. We were then chasing the game with 10 men. That made it difficult for us and they kept the ball well to see the game out.
"I haven't seen the penalties back again but from where I was standing on the pitch I don't think we can argue with them."
