Wigan were relegated from the Sky Bet Championship after losing to Reading while the line-up for the play-offs was all but confirmed on the penultimate weekend of the regular season.
The Latics were promoted from League One last season but face another stint in the third tier after Yann Kermorgant's sixth-minute effort gave the Royals a 1-0 victory at the Madejski Stadium.
Kermorgant, 35, headed home his 17th goal of the season early on and although the visitors battled manfully, they could not find a way back into the contest.
Now seven points adrift of safety, with Blackburn and Birmingham both winning, Wigan join Rotherham in dropping out of the division next season.