Muscat, recently signed from Glasgow Rangers, was given a red card for an off the ball incident in which he stamped on Watford striker Danny Webber.
"He's a nice person off the field but once he steps on to the pitch he tends to do daft things," said Watford boss Ray Lewington who handled the player at Crystal Palace when he was coach.
Millwall boss Mark McGhee said: "I haven't asked for a reason because there can't be a reason. It was an insane act. Just crazy."
Millwall had clawed their way back after falling behind in the ninth minute and looked the better side.
Watford's Gavin Mahon sent over a cross for Lee Cook to head back for Bruce Dyer to slot in from close range for his first goal of the campaign.
Webber wasted a good chance of adding to the score when sent clear and a minute later Millwall grabbed an equaliser. Tony Craig's long throw was headed on by Bob Peeters and Paul Ifill met the ball with a close-range volley.
But on the stroke of half time Muscat handed Watford a penalty and skipper Neil Cox sent keeper Tony Warner the wrong way as he rolled home the spot-kick.
Millwall worked hard with ten men but were unable to really conjure a shot until the 80th minute when sub Doug Livermore fired over from just outside the box.
Tim Cahill forced Alec Chamberlain to a fine save when he hooked a Darren Ward flick goalwards, but Warner was the busier of the two keepers.
After 89 minutes Watford cemented their first victory of the campaign when debut-making Paul Devlin saw his cross deflected to the far post for 18-year-old Ashley Young to score from close in, 15 minutes into his debut.