The 21-year-old, who hails from Ormskirk, was expected to join Championship rivals Barnsley ahead of Thursday's 5pm deadline.
But Latics jumped to the head of the queue for the defender, who joined Leeds in 2014 after being released by Everton as a 16-year-old.
Pearce, who has represented England at Under-20 and Under-21 level, spent the second half of last term on loan with League One Scunthorpe.
He will provide competition at Latics for Antonee Robinson, who was a team-mate throughout the Everton youth ranks.
The fee is understood to be in the region of £300,000.