Ronaldo converted an 88th minute penalty, after Tim Cahill had cancelled out the Portuguese's opener.
United reached 42 points to remain in pursuit with leaders Arsenal, while Everton, who suffered their first defeat in eight games, are sixth with 30 points.
Ronaldo opened the scoring after 22 minutes with a wonderful left-footed drive after a clever dummy to Lee Carsley.
However, Australian playmaker Tim Cahill leveled the scoring after just four minutes when he superbly rose above Patrice Evra to head in his fourth of the season.
Clumsy Pienaar
The Toffees were within a whisker of sealing a point against a United side who have proven to be lethal at home this season.
However, a lazy challenge by South Africa midfielder Steven Pienaar on Ryan Giggs gave the referee no option but to point to the spot.
Ronaldo made no mistake from the spot to hit his fourth brace this season and put his name on top of the Premiership scoring charts with 11 goals.