The French striker bagged a treble of goals in just seven second-half minutes in Croatia, beating the record previously held by former Blackburn forward Mike Newell
The 26-year-old was on hand to help the French side complete an unlikely escape from Group D by netting four crucial goals, three of which were within a seven minute period.
His exploits have now earned him the honour of the quickest-ever hat-trick in Europe's elite club competition, which was previously held by Mike Newell.
The former Blackburn Rovers man netted three in a nine-minute spell during the Lancashire outfit's Champions League encounter with Rosenborg in 1995.
Lyon had begun the night requiring a seven goal swing to go through at the expense of Ajax after goal difference took precedence over head-to-head following two nil-nil draws with the Dutch side.
Gomis' heroics in Lyon's 7-1 win, couple with Ajax's 3-0 loss to Real Madrid, meant the French side qualified with a goal difference of 2 ahead of Frank De Boer's side, who finished with 0.
Valencia attacker Roberto Soldado also made history during the 2011-12 group stage campaign after scoring the quickest Champions League hat-trick since 2003.
The Spanish forward grabbed a 38-minute treble against Genk during a Group E showdown.