Lee turned the tables against one of the nation's best kick-blocking teams with just 1:52 remaining.
The Hokies had scored two points on Stephan Virgil's 98-yard touchdown return of a third-quarter extra point block attempt.
Quarterback Pat Pinkney threw for one touchdown on 19 of 23 passing for 211 yards.
The Pirates' Brandon Simmons rushed for 54 yards on 17 carries, while Jonathan Williams added 48 yards on 10 rushing attempts.
Tech quarterback Sean Glennon completed 14 of 23 passes for 139 yards with two interceptions.
Virgil returned a second-quarter kickoff fumble 30 yards for a touchdown and Kenny Lewis scored on a six-yard run in the second quarter for the Hokies (0-1), whose six-game winning streak against the Pirates ended.
The contest was played at a neutral site, the Carolina Panthers' Bank of America Stadium in Charlotte.