Wolves had taken the lead in the first half when Seyi Olofinjana slotted past Graham Stack after Kenny Miller's pass.
Millwall hit back and Michael Oakes saved from Jody Morris before Dennis Wise netted from the spot after Joleon Lescott had fouled Barry Hayles.
But Seol slammed a low shot into the corner from 25 yards in stoppage time to dent the Lions' play-off ambitions.
Millwall assistant boss Ray Wilkins:
"It's not a factor whether you deserve a point; you have to get one.
"I'm disappointed that our players didn't protect Graham Stack enough - but you have to compliment them on their win.
"We have a great bunch of players. They work very hard, and I am sure we will be there or thereabouts at the end of the season," said Wilkins.
Wolves boss Glenn Hoddle:
"With players like Seol in the team, we have a get-out clause - because he has that pace and skill.
"Since I took over as manager, he has scored goals for us and created chances as well.
"We changed his position slightly against Millwall, and he adapted well; Seol has a few strings to his bow," said Hoddle after a third straight win.
Millwall: Stack, Lawrence, Phillips, Ward, Livermore, Muscat, Morris (Wise 59), Dunne, Hayles, Dichio, Dobie (Ifill 57).
Subs Not Used: Serioux, Marshall, Elliott.
Goals: Wise 77 pen.
Wolverhampton: Oakes, Clyde, Lescott, Craddock, Naylor, Kennedy, Olofinjana (Andrews 81), Ince, Seol, Cort, Miller (Clarke 65).
Subs Not Used: Ikeme, Newton, Bjorklund.
Booked: Clyde, Olofinjana, Lescott.
Goals: Olofinjana 37, Seol 90.
Ref: K Hill (Hertfordshire).