Aitor Karanka's side needed a point to guarantee second place in the table and automatic promotion behind Burnley, and they took a deserved lead through Cristhian Stuani in the first half.
Brighton levelled after the break but goalscorer Dale Stephens went from hero to villain in the space of four minutes as he earned a straight red card for a high challenge on Gaston Ramirez.
Chris Hughton's side battled hard in search of the goal they needed to leapfrog their opponents, but Boro held on to seal their spot back in England's top flight - an achievement expected to earn the club at least an extra $332 million in revenue next season.
Karanka raised eyebrows when he left Jordan Rhodes and Stewart Downing out of the starting line-up, but it was the two men who replaced them who combined to give Boro the lead after 19 minutes.
Ramirez's free-kick was headed back across goal by David Nugent, allowing Stuani to tap home from point-blank range.
Stuani and Ramirez both came close to a second as Boro continued to dominate the first half, but Brighton made them pay for their profligacy just after the break when Stephens turned a looping header beyond Dimitrios Konstantopoulos to equalise.
Stephens was then involved in a heated spat with Ramirez and was sent off shortly afterwards after catching the Uruguayan on the shin with a raised boot - a challenge which resulted in a tearful Ramirez being carried from the pitch on a stretcher.
Nerves became frayed around the Riverside as Brighton pushed forward for a lifeline during eight minutes of injury time, but Hughton's side must now settle for a place in the play-offs against Sheffield Wednesday.
