The meeting, which took place in Porto at the Dragau, ended with a score of 3: 0 in favor of the home team.
Porto won with goals from Moussa Marega, who scored in the 4th minute, Sergio Oliveira, who converted a penalty in the 28th minute, and Luis Diaz, who scored in the 69th minute.
Dimitri Payert missed the penalty in the 10th minute for Marseille.
In the fourth round, Porto and Marseille will play at the Velodrome.
The match will take place on November 25.
Earlier it was reported that Ajax won their first win in the Champions League season, beating Midtjylland.