The prosecution was intended by authorities to signal a new seriousness in tackling pollution from cruise ships after a spot check in March on The Azura, operated by P&O Cruises, found it contained unauthorised bunker fuel.
American captain Evans Hoyt knew that the fuel was illegal -- it contained 1.68 per cent sulphur, above the 1.5-per cent European limit -- and the company was using it to save money, prosecutors said during the trial.
The judge handed Hoyt a fine of 100,000 euros but specified that the parent company of P&O, US-based cruise giant Carnival, should pay 80,000 euros of the sum.
The company had "wanted to save money at the expense of everyone's lungs," prosecutor Franck Lagier told the court in October.
Marseille is a popular stop-off for giant cruise ships that ply routes in the Mediterranean between Spain and Italy and port services are an important part of the local economy.
But the city has struggled with increased smog in recent years and shipping is thought to be responsible for a large part of the pollution, which causes respiratory problems and lung disease.
High-sulphur fuel, which is cheaper than cleaner versions, produces sulphur oxides which contribute to acid rain and the acidification of oceans.
(With inputs from agencies.)