Wednesday were unhappy their advantage after an absorbing contest at Hillsborough was not more convincing after a controversial first-half episode saw another goal from Fernando Forestieri ruled out for offside.
Yet the two goals, a thunderous strike from Wallace just before halftime, and an expertly-taken 73rd minute finish from Lee, were a deserved reward for the Yorkshire side's superiority over the Seagulls and changed the mood completely.
Brighton, who finished third in the regular season and missed out on automatic promotion on goal difference, must now become the first side in a Championship playoff to overcome a two-goal deficit when the sides meet again at the Amex Stadium on Monday.
The Owls, fifth in the regular season, were enraged when Forestieri's 19th-minute goal was disallowed after a delayed decision by the linesman although he was later shown by TV replays to have been correct.
The winners will play Derby County or Hull City, who play their semi-final first leg on Saturday, in the final at Wembley on May 28. The victors will then be rewarded with a Premier League place.
(Reporting by Ian Chadband; Editing by Tony Jimenez)
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