The battle between two teams struggling at the bottom end of the table was settled in favour of West Brom thanks to Kyle Bartley's goal in the 11th minute.
However, Lewis Dunk's quickly taken free-kick appeared to have drawn Brighton level in the first half, his attempt coming with goalkeeper Sam Johnstone still situated by his post while lining up a defensive wall for the home team.
Mason, who had appeared to blow his whistle to allow the game to be restarted, initially awarded the goal, then disallowed the strike instead.
A further delay in proceedings then followed when the on-field official was told to check the pitch-side monitor after communication with video assistant referee (VAR) Simon Hooper.
The check appeared to be concerning the possible presence of an attacking player in an offside position, though it was then announced the goal had been ruled out as Mason had actually sounded his whistle for a second time before the ball crossed the line.
Dunk, however, was far from impressed by the eventual outcome.
"It's embarrassing, it's a horrendous decision," the Brighton captain said. "I said to the referee, 'Can I take it?'. He blew his whistle and I took it.
"I don't think he knew what he was doing. He gave the goal, why did he give it? I don't know why VAR was getting involved, he said: 'Goal'. You can look on the video, if you want."
Asked if Mason lost control of the game, the defender replied: "Yeah he did. Fact."
Brighton slipped to defeat at the Hawthorns despite having more than 70 per cent of possession and 15 attempts.
It also contrived to waste not one but two penalties, in the process becoming the first team in Premier League history to miss two spot-kicks by hitting the woodwork in a single game.
Pascal Gross squandered the first opportunity from 12 yards out in the opening half, while Danny Welbeck was also unsuccessful in the 75th minute having taken over penalty duties for the visitors.
The Seagulls will return south wondering quite how they managed to come away without anything from the fixture, but victory for West Brom boosts its survival hopes.
Sam Allardyce's side remains 19th on the table but it has closed the gap down to eight points on 17th-placed Newcastle United, which sits a point and a place below Brighton ahead of hosting Wolverhampton Wanderers later in the day.
Offering his version of events over the free-kick goal that never was, match-winner Bartley said: "The ref blew his whistle he said to speak to someone in the wall, there was a bit of pushing.
"There was a bit of confusion but Lee Mason dealt with it really well and came to the right conclusion. It was a bit confusing, I don't think it would have been right for them to score like that."