The Welsh superstar's header was his first goal of his second spell at Spurs and his first for the club in more than seven years, in a match that was marred by refereeing and VAR controversy.
After Harry Kane gave Tottenham the lead from the penalty spot early in the match, Brighton flyer Tariq Lamptey scored the equaliser in the second half despite Seagulls wing-back Solly March bringing down Pierre-Emile Hojbjerg in the lead-up.
VAR operator Jonathan Moss alerted Scott to the possible foul in the build-up to Lamptey's goal and asked the referee to come to the pitch-side monitor to review March's tackle.
Despite footage of the incident suggesting March brought down Hojbjerg without touching the ball, Scott ruled that Lamptey's goal should stand after viewing the incident for 70 seconds - much to the frustration of Tottenham's players.
When asked about the decision after the match, Mourinho said his view 'doesn't matter' but made it clear he was unhappy by suggesting Scott should attend a press conference to explain the call.
"I prefer to stay away [from VAR]," Mourinho said to Sky Sports.
"Probably the referee should go to the press conference and explain. He had time to go to the screen so only he can explain why it is a goal. He is a good ref and a good guy, only he can explain that decision. My view doesn't matter."
Lamptey's goal wasn't the only controversial moment involving VAR, with Brighton's Leandro Trossard having a penalty appealed dismissed by Moss after a review.
Trossard was clearly held by Spurs defender Matt Doherty as the low cross flashed through the box, with the Belgium international falling to floor when he was released by his opponent.
Tottenham's victory sees the team climb to second on the Premier League table, two points behind leaders Liverpool.