Thousands of Polish supporters swarmed through the narrow streets of the city's Vieux Port (Old Port) district, drinking, chanting and letting off smoke bombs before the match.
Fighting erupted suddenly among a group of hardcore Polish fans and was swiftly quelled by police deployed around the waterfront.
Officers led supporters away in handcuffs, according to a Reuters photographer. A police official said the fights involved rival Polish hooligan groups.
Polish and Ukrainian fans were also involved in skirmishes outside the stadium before the game. Police intervened with tear gas and water cannon and arrested those involved in the fight.
Poland beat already-eliminated Ukraine 1-0 to advance to the knockout stage for the first time. They will be play Switzerland in the next game.
Marseille authorities deployed about 1,000 police and 200 private security agents for the match. A surveillance helicopter hovered over the fan zone close to the stadium.
Fan violence marred the opening days of the tournament and forced European soccer's governing body UEFA to threaten England and Russia with expulsion from the championship. But disturbances have largely subsided in recent days.
In the southwestern French city of Bordeaux, Irish supporters, who have endeared themselves to the French with their warm-hearted banter, serenaded officers with chants of: "Stand up for the French police."
And in Paris, German and Northern Ireland fans marched, chanting and drinking beer, to the stadium where their teams were to face off at 6 p.m. (1600 GMT).
UEFA fined the Hungarian soccer federation 65,000 euros (49,913.01 pounds) for crowd trouble at Euro 2016, the European football's governing body said on Tuesday.
The charges related to "crowd disturbances, setting off of fireworks and throwing of objects" during the 1-1 draw against Iceland in Marseille on Saturday.
(Additional reporting by Jean-François Rosnoblet in Marseille and Julien Pretot in Paris; Writing by Ingrid Melander; Editing by Richard Lough and Mark Heinrich)
