Big-spending Paris St Germain, who spent millions to bring in European greats including Zlatan Ibrahimovic, were held to a boring goalless home draw by Bordeaux.
Marseille, who were disappointed with their 10th place finish last season, are on nine points while Montpellier lie 18th with one point, without a win after three games for the first time since the 1997-98 season.
Bordeaux are fourth on seven, tied with second-placed Lyon. PSG are 11th on three points.
In Montpellier, in-form Gignac netted from the left on 77 minutes thanks to a blunder from goalkeeper Geoffrey Jourdren, after Morgan Amalfitano took advantage of a Daniel Congre mistake to steal the ball just outside the box.
"At the moment, we do not make the good choices, we make mistakes when we cannot afford to," Montpellier's coach Rene Girard told reporters.
"We can not say we are serene but we will not panic. Now we will see how strong we are. Everybody needs to give a bit more."
The match failed to match its billing as the first high-profile encounter of the season, consisting of a series of technical errors and missed opportunities.
Despite playmaker Younes Belhanda returning from injury, Montpellier struggled to unsettle their rivals.
Their best chance came on 37 minutes when Belhanda hit the woodwork after a fine one-two with Romain Pitau.
Montpellier tried to increase the pace after the break but never really threatened Marseille, who controlled the hosts to claim their third win in a row.
PSG had much more control than Montpellier but were muzzled despite Ibrahimovic's efforts up front, a week after a poor collective showing at Ajaccio.
The Swede, whose brace for his debut in France saved his side from a defeat two weeks, had the best chance in the second half but his powerful free-kick went wide on 52 minutes.
The former AC Milan striker showed several signs of irritation with his team mates as a flurry of passes were not picked up.
At Saint-Etienne, Romain Hamouma shone as the hosts hammered Brest 4-0 home to clinch their first victory of the season.
The tricky winger set up Pierre-Emerick Aubameyang in the box for the opener on 13 minutes, then poked the ball home in the 30th minute after Aubameyang hit the post.
Josuha Guilavogui scored the third after 61 minutes and Aubameyang wrapped it up a minute later.
Saint-Etienne climbed to 10th on three points.
- Zlatan Ibrahimovic