Ronaldo, who finished second to AC Milan's Brazilian midfielder Kaka for European Golden Ball award on Sunday, scored in the 10th and 58th minutes at Old Trafford to increase his season total to 13 goals in 11 games. It also gave him six in his last four appearances against Fulham.
Ronaldo appeared certain to score a third with 12 minutes remaining when he appeared to get around goalkeeper Antti Niemi. But he went down under the goalkeeper's challenge and was shown a yellow card for a dive, a decision that infuriated manager Sir Alex Ferguson.
"The penalty kick incident is the result of a perceived idea of the referee that Ronaldo dived, there's no question about that," Ferguson said.
"In this case, the goalkeeper has conned the referee. There's no question the goalkeeper got Ronaldo booked. Why would he dive? It's a ridiculous decision."
The United manager was disappointed his team didn't score more.
"It was a comfortable 2-0 win even though Fulham had a lot of possession in the game," Ferguson said. "Too many chances missed.
"It was a reasonable performance. When we put our foot on the gas, we looked as if we could score goals all the time."
United's 10th victory of the season gave it 33 points from 15 matches, moving it back in front of Chelsea and Liverpool - both of which won over the weekend - and three points behind Arsenal.
Arsenal, which is unbeaten with 11 wins and three draws, could move six points ahead with a victory at Newcastle on Wednesday in a rescheduled match.
Monday's loss left 14th-placed Fulham two points above the relegation zone.
Wayne Rooney returned after missing three matches for United - as well as two England - with an ankle injury and partnered Carlos Tevez in attack.
United took only 10 minutes to go ahead when Fulham midfielder Steven Davis, attempting to a clear a corner, headed it to Nemanja Vidic who set up an unmarked Ronaldo for a 12-yard volley.
As the home side maintained the early possession, Fulham goalkeeper Niemi twice was forced into dramatic saves to thwart Tevez.
Nieme's United counterpart, Edwin van der Sar, likewise made a diving save against his former club to deny Danny Murphy, and Shefki Kuqi headed wide four minutes before halftime.
Ronaldo added the second in the 58th minute when he got ahead of Fulham defender Aaron Hughes to meet a cross from John O'Shea and converted with a downward header.
Fulham manager Lawrie Sanchez responded by inserting former United striker David Healy for Clint Dempsey to field two strikers.