Marseille added there had been "unacceptable behaviour" from some fans who subjected Evra and his team-mates to "hateful attacks" but said: "As a professional and experienced player, Patrice Evra could not respond in such an inappropriate way".
The ex-Manchester United left-back, who joined Marseille from Juventus in January, was among the substitutes for the Group I match in Portugal.
When some of the Marseille fans began approaching the pitch, the rest of the Marseille team ran over, and Evra aimed a high kick over the advertising boards towards a fan standing on the other side.
"Olympique de Marseille has noted the altercation between an individual and Patrice Evra in the warm-up of players during the match against Guimaraes", it read.
At 36 years old, with his play declining, this incident might be career-ending for Evra.
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The referee apparently saw the incident and red carded Evra before the game even started.
Evra has been charged with violent conduct by UEFA, while Marseille have also been charged with a field invasion by fans, setting off of fireworks and "acts of damages".
"An internal investigation will be carried out to establish all responsible", it stated.
It sparked wild scenes as Evra fought back, lashing out at one supporter with an apparent kick to the head, and Garcia had some advice for the 81-time France worldwide.
"Pat has experience and he must not react, it's obvious", Garcia was quoted by L'Equipe as telling BeIN Sports.