The supporters’ group Paris Ultras Collective said in a statement that Lyon fans attacked a bus carrying PSG supporters while the two sides’ fans were supposed to be taking different routes.
Police did not indicate which group of fans launched an attack.
Traffic on the major north-south A1 highway was interrupted in both directions.
Heavy security
Mingling with the public in nearby Tourcoing ahead of the game, Mr Macron said he “condemns all violence with the greatest firmness”, adding: “I hope that things will go as normally as possible this evening.”
Olympique Lyonnais (Lyon) said in a statement it “condemns this violence”. The French Football Federation called the violence “unacceptable”.
After the match later in Lille, supporters left the stadium calmly, amid a heavy police presence.
Earlier fans of the rival teams mingled all day without incident ahead of the 9pm (7pm GMT) start time.
The regional police authority said 1,000 officers were on duty in the town and a further 1,000 in the stadium.
The local authorities had also put in place a number of measures for the high-risk match.
Fans were forbidden to move “outside the areas reserved for them” near the stadium until 4am local time on Sunday, and authorities banned the public consumption of alcohol “in a glass or metal container” until the same time.