Waghorn, a substitute against Millwall on Tuesday, was sent off within eight minutes of coming on and his subsequent three-match ban will keep him out for the rest of the season.
His next game in a Latics shirt will definitely come in Sky Bet League One if they fail to beat the Seagulls, but defender Pearce is eligible to feature after the three-match ban he was awarded following his own red card was overturned.
Gary Caldwell, who remains without Emyr Huws (ankle) and Grant Holt (knee), is still seeking his first win as a boss and will have Josh Murphy available after he extended his loan from Norwich.
Brighton, still not mathematically safe themselves, will be without Joao Teixeira.
The on-loan Liverpool midfielder’s season is over after he suffered a broken leg during Tuesday night’s goalless draw with Huddersfield.
Sam Baldock, Andrew Crofts (both knee), Kemy Agustien (thigh) and Solly March (calf) are also on the sidelines.
Skipper Gordon Greer is pushing to return in defence after he was an unused substitute in midweek following his return from a two-match ban.