Van der Sar's total now stands at 1,124 minutes, but United manager Sir Alex Ferguson will be more excited by the result than the record.
United secured the points with Ronaldo 's 14th goal of the season - a 44th minute penalty.
The win took the Reds five points clear of Liverpool and Chelsea, who meet at Anfield on Sunday.
Referee Mark Halsey awarded the penalty after Mikel Arteta caught Michael Carrick 's ankle as he raced on to a Carlos Tevez flick inside the Everton box.
Ronaldo stepped up to blast his right-foot spot-kick almost straight into the back of the net with Everton goalkeeper Tim Howard diving to his right.
Everton must have felt a sense of deja vu as last season's Old Trafford meeting between the teams was also decided by a Ronaldo penalty when Steven Pienaar upended Ryan Giggs.
United deserved their victory, but it was hard-fought against an Everton side which is one of the hardest to break down in the Premier League.
United had been denied three times before breaking the deadlock - twice by Howard and once by a post.
In the 13th minute, Ronaldo's cross from the left was headed away by Joleon Lescott .
The ball fell to Ji-Sung Park just inside the Everton box and he found Tevez six yards out, but the Argentinian's snap-shot was brilliantly saved by Howard from point-blank range.
Eleven minutes later, Ronaldo's well-directed toe poke from 20 yards out hit the foot of an Everton post and Howard produced another fine stop soon after to tip over the Portuguese winger's dipping drive from 20 yards.
The Red Devils should have had a second penalty three minutes after the interval when Carrick was again brought down in the Everton box, this time by Lescott, but Mr Halsey waved away the appeals.
Van der Sar was called into action on the hour to keep out Arteta's fierce 35-yard free kick, but Howard was again the busier goalkeeper in the second half, twice denying Tevez.