Rooney's 77th minute strike and Ronaldo's 23rd of the season, 17 in the league, on the final whistle proved vital as nearest challengers Arsenal won 3-0 at relegation strugglers Fulham and Chelsea also squeezed out a 1-0 victory at Birmingham.
Reading played their part in an entertaining match at their Madejski Stadium and often troubled United, but Rooney provided a vital breakthrough and as the home side searched desperately for an equalizer, Ronaldo sealed the three points.
It took a moment of magic from Argentine Carlos Tevez to supply a killing pass for Rooney to score his sixth league goal of the season while Reading's Kevin Doyle went close with a header before Ronaldo scored on a breakaway.
United manager Alex Ferguson was relieved by the late strikes:
"Considering the number of opportunities we had, maybe our decision-making in the final third of the field wasn't at its best.
"We kept making chances, but you do start to worry when the game goes on and you haven't scored.
"Credit to Reading, they keep going at you all the time and I think that's an important result for us," he said.