His three goals in seven minutes, including the first just before half-time, meant the France striker beat the previous record set by Blackburn Rovers' Mike Newell in December 1995.
The 7-1 scoreline in Group D, which put Lyon through to the knockout stages for a ninth straight season, was also the French club's biggest win in the Champions League and Dinamo's heaviest defeat in all European competition.
Remi Garde's side also needed Ajax Amsterdam to lose at home to Real Madrid and hope for a seven-goal swing in goal difference which they managed comfortably as Ajax went down 3-0.
Gomis scored a fourth as he became only the seventh player to reach that tally in one Champions League match.
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