Paul Scholes gave United the perfect start in their quest to reach the knockout stage with a close-range finish after only six minutes.
But Geovanni's diving header quickly put Benfica level and Beto fired in a second from 20 yards before half-time.
United's best move of the game almost produced the equaliser after 57 minutes, when Scholes and Van Nistelrooy linked and set up Ronaldo, but he pulled a tame finish across the face of goal.
Ferguson gambled with two substitutions in quick succession, replacing Giggs with Louis Saha and sending on Park Ji-Sung for Ronaldo.
And as United pressed forward, Benfica almost punished them on the counter-attack as substitute Joao Pereira shot wastefully into the side-netting with only Van der Sar to beat.