Jose Mourinho got the best out of Harry Kane and Son Heung-min who thanked their sacked Tottenham manager.
Molde took a surprise lead at Emirates Stadium, but Arsenal fought back to make it three Europa League wins from three.
Brendan Rodgers' men extended their perfect start in the Europa League by thrashing their main rivals for top spot in Group G.
Zlatan Ibrahimovic was taken off after an hour as Milan slumped to their first defeat of the season, with Yusuf Yazici starring at San Siro.
Harry Kane scored one and set up another in his 45 minutes on the pitch against Ludogorets, reaching 200 Tottenham goals in the process.
Atletico Madrid won the Europa League with a 3-0 victory over Marseille, as Antoine Griezmann played a starring role.