Moussa Marega opened the scoring after four minutes and Sergio Oliveira doubled the advantage for the hosts after 28 minutes from the penalty spot.
Luis Diaz added the third midway through the second-half at the Estadio do Dragao to inflict a third consecutive loss on the Ligue 1 outfit.
Marseille lie bottom of Group C after three games with an unenviable record of 12 consecutive defeats in the Champions League starting in the 2011/12 season.
1 - Worst run of consecutive defeats in the CL history (since 1992/93) :
— OptaJean (@OptaJean) November 3, 2020
12 - 🇫🇷 Marseille between 2012 & 2020 (current run)
12 - 🇧🇪 Anderlecht between 2003 & 2005
Painful. pic.twitter.com/Gu2VKrqSbB
Porto are second with six points while Manchester City set the pace following a 3-0 win over Olympiakos at the Etihad Stadium.
Ferran Torres was on target for Pep Guardiola’s side in the first-half. Gabriel Jesus and Joao Cancelo secured the points with strikes in the last 10 minutes.
Elsewhere, the defending champions Bayern Munich scored four in the last 11 minutes to overpower Salzburg 6-2 in Group A
Just as a stalemate loomed, Jerome Boateng grabbed Bayern's third. Leroy Sané added the fourth and in the closing minutes Robert Lewandowski got his second of the game and Lucas Hernandez added the gloss.
Jota on song
The 2019 champions Liverpool were also in expansive mood. They thumped Atalanta 5-0 to maintain their 100 percent record in Group D. Dioga Jota scored a hat trick in the rout. Sadio Mané and Mohammed Salah added the others.
Ajax climbed to second following their 2-1 win at FC Midtjylland
And in Group B, a goal from Rodrygo in the 80th minute spared Real Madrid's blushes after they let slip a 2-0 lead over Inter Milan.
Karim Benzema and Sergio Ramos put Zinedine Zidane's men in the driving seat before Lautaro Martinez halved the deficit just before the pause.
Martinez set up Ivan Perisic for the equaliser in the 68th minute before Rodrygo's intervention.
Madrid climb to second in Group B behind Borussia Moenchengladbach. Alassane Plea scored three as the Bundesliga outfit thumped Shakhtar Donetsk 6-0 to go top of the pile.
