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.
United were missing ever-presents Nemanja Vidic and Wayne Rooney, but while Barca dominated possession, it was the hosts that always looked the more likely to add to Scholes' opener.
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.