VIDEO: Boss and Stears on Wolves' finale
Watch Wolves boss Kenny Jackett and acting captain Richard Stearman's post-match interviews after missing out on a Championship play-off spot.
Nouha Dicko (20 and 56 minutes), Ethan Ebanks-Landell (70) and Bakary Sako on the stroke of full-time scored Wolves' goals.
Replies from Aiden O'Brien (58) and debutant Jamie Philpot (82) for Millwall made things more tight than they might have been.
Derby, surprisingly, went down 3-0 at home to Reading to finish eighth, from being title favourites earlier in the campaign.
Brentford's 3-0 victory at home to relegated Wigan and Ipswich's 3-2 defeat at Blackburn saw Wolves miss out on goal difference, four below than Ipswich Town.
Dicko's brace took his tally to 14 in the league and 15 overall, the tally Sako ended on in the Championship, for what is expected to be his final appearance in gold and black.
Both players along with Richard Stearman were named as the three contenders for Player of the Year, which will be announced at the annual awards dinner at Telford International Centre on Wednesday.
