Picking up the ball from Gomez midway inside the visitors' half, the Australian full-back strode forward into the space as it opened up for him before hitting a swirling shot from 25 yards that bamboozled Richard Wright in the Ipswich goal and flew in off the underside of the bar.
It was perhaps a little more than Wolves deserved, if not their patient supporters. Deprived of their first-choice strikers, Robbie Keane and David Connolly, through flu and tendinitis respectively, Lee was obliged to pair the willing Neil Emblen with a weary looking Guy Whittingham.
Neither player made much headway against the meanest defence in the First Division and if the game was diminished as a spectacle by Wolves' absentees there was a further blow to the neutral when Ipswich's highly rated under- 21 international midfielder, Keiron Dyer, pulled a hamstring in the first five minutes.
Dyer struggled on for 20 minutes before finally making way for Marco Holster and the game promptly died a death until Muscat offered a hint of things to come with a shot that went just over the crossbar after an hour. His fellow full-back, Mark Atkins, might have done better than to poke the ball wide a few minutes later. Then Gomez came on and the action began.
Robert Niestroj, playing his first full game for Wolves since signing from Borussia Dortmund, had a far-post effort blocked on the line before Gomez hit the bar with a rasping shot from the ensuing corner. Whittingham and Emblen then both went close before Ipswich, who were frankly disappointing, had their best chance with five minutes to go but defender Manuel Thetis shot straight at Mike Stowell. Almost immediately Matt Holland's goal-bound shot was desperately blocked by Muscat who, suitably inspired, roamed upfield to make the decisive contribution.
Goal: Muscat (88) 1-0.
Wolverhampton Wanderers (4-4-2): Stowell; Atkins, Curle, Richards, Muscat; Niestroj (Corica, 89), Robinson, Osborn (Gomez, 70), Sedgley (Gilkes, h-t); Whittingham, Emblen.
Ipswich (3-4-3): Wright; Thetis, Mowbray, Venus; Kennedy (Logan, 90), Dyer (Holster, 25), Holland, Clapham; R Naylor, Abou, Johnson. Substitute not used: Bramble.
Referee: M Halsey (Welwyn Garden City).
Bookings: Wolves Niestroj; Ipswich Kennedy.
Man of the match: Muscat.