The meeting of French football’s biggest rivals was briefly held up on more than one occasion as objects were thrown from the stands when PSG players went to take corner kicks.
There was another interruption in the second half when one young man invaded the pitch and approached Messi before being escorted off by a legion of security staff.
It was that sort of night for PSG, who could not get into their stride and were reduced to 10 men when Achraf Hakimi was sent off in the second half following a VAR review for a last-man challenge on Cengiz Under just outside the box.
The game was also marked by two goals disallowed in the first half for tight VAR offside decisions, one an own-goal by Marseille defender Luan Peres and another at the opposite end from Arkadiusz Milik.
It is a perfectly acceptable result for Mauricio Pochettino’s side, who have lost just one of their opening 11 matches in Ligue 1 and are seven points clear at the top from Lens in second.
“I think we played very well, but we just couldn’t get the goal,” Pochettino told broadcaster Amazon Prime.
“The team showed great character, and of course identity and style.”
However, the performance of PSG’s attacking superstars will again come in for scrutiny.
Pochettino selected Messi, Neymar and Angel Di Maria in a line of three behind Kylian Mbappe but that quartet was kept quiet for most of the game by a hard-working Marseille side.
“I thought we deserved the three points today because we were better than them,” insisted Marseille’s on-loan Arsenal midfielder Matteo Guendouzi.
Messi was coming up against Jorge Sampaoli, who coached the six-time Ballon d’Or winner at the 2018 World Cup when in charge of Argentine, and who is now on the Marseille bench.
The former Barcelona man scored twice for the Qatar-owned club in their 3-2 midweek win over RB Leipzig in the Champions League, but here he rarely looked finding the net.
A close-range header that was tipped over by home goalkeeper Pau Lopez in the first half was the closest Messi came.
All of his three goals in a PSG shirt have come in the Champions League, while he is yet to score in four Ligue 1 appearances.
Hakimi sent off
The visitors, deprived of any travelling support amid concerns about potential crowd disorder, thought they had gone in front in the 14th minute.
Neymar’s ball across goal looking for Mbappe was turned into his own net by Peres, but the goal was disallowed for an offside against the world’s most expensive player.
Milik then had a goal at the other end ruled out midway through the first half.
The Polish striker controlled a low ball and fired in but the goal did not stand because Pol Lirola was just offside before crossing.
PSG lost Marco Verratti to injury just before half-time and had Hakimi sent off in the 57th minute for shoving over Under, a yellow card upgraded to red after another VAR review.
Di Maria was sacrificed to allow Pochettino to send on another defender and Marseille had chances, with Valentin Rongier and substitute Konrad de la Fuente both missing from close range.
Mbappe was denied by a brilliant William Saliba challenge at the other end, and Marseille are fourth with a game in hand.
Earlier Lens beat Metz 4-1 to stay second, with Wesley Said scoring twice, while Nice are third after coming from two goals down to beat Lyon 3-2.
Karl Toko-Ekambi and Houssem Aouar scored for Lyon, but Youcef Atal got one back for Nice with nine minutes left before Lyon had Tino Kadewere sent off.
Andy Delort equalised with a penalty in the 89th minute and 20-year-old forward Evann Guessand won it in stoppage time for the home team.
There were also wins for Monaco, Rennes and Troyes.