West Ham won 3-1 afte Enzo Fernandez missed a penalty to send Chelsea 2-1 up.
The goal made Bowen the first English player to score the winner in a major European final since Arsenal's Alan Smith in 1994 and capped a campaign in which West Ham were unbeaten in 15 UEFA Europa Conference League matches.
Arsenal have 74 points from 31 games with reigning champions Manchester City on 70 having played a game less.
Lampard's last game in charge was Saturday's 2-0 league defeat at West Ham United, which kept Everton second-bottom of the table on 15 points after 20 games, above Southampton on goal difference, and two points adrift of the safety zone.
John Lundstram struck 10 minutes from time to give Rangers a 3-1 win over RB Leipzig and send them into the final 3-2 on aggregate after a see-saw clash at a rocking Ibrox.
Atalanta goalkeeper Juan Musso saved a penalty and a follow-up attempt but he couldn't keep out an own-goal by Davide Zappacosta from the resulting corner as Leipzig salvaged a 1-1 draw.
Arsenal's third successive league win lifted them above West Ham United into fifth place with 45 points, one behind Manchester United but having played two fewer games.
Minamino came off the bench to score in a 3-0 win for Jurgen Klopp's side.
The Hammers moved within a point of fourth-placed Arsenal.
West Ham came from behind twice and then claimed all three points with a late goal from substitute defender Arthur Masuaku.