Scholes' piledriver came in the 14th minute for United and while Barcelona threatened, the visitors couldn't find a way past a patched-up defence over the 90 minutes.
Nani, either side of halftime, had chances to extend United's lead, while Carlos Tevez, outstanding on the night, had a shot saved after a wonderful interchange with Cristiano Ronaldo midway through the second-half.
United made the breakthrough in the 14th minute with a wonderful effort from the evergreen Scholes.
He rattled a shot from 25 yards beyond Victor Valdes to put United 1-0 ahead on aggregate with his first goal in the competition this season.
Scholes, making his 101st Champions League appearance, took full advantage after Barcelona failed to clear their lines following a surging run from Ronaldo.
Henry almost returned to haunt United with a point-blank header from from Xavi's corner which was gratefully clutched by Edwin Van der Sar.
Barcelona weaved pretty patterns in the closing stages, but United's defence - superbly marshalled by Rio Ferdinand and Wes Brown - stood firm to spark wild scenes of celebration at the final whistle.
While Patrice Evra was stretchered off in injury-time with a head injury, United's players avoided suspension for the final in Moscow.