Chirac demanded an apology for the jeering
The start of the match at the Stade de France in Paris had to be delayed by about 20 minutes after Mr Chirac demanded that the booing stop and that the French Football Federation apologise to the nation.
A furious Mr Chirac told a live television audience that the booing and whistling was an insult to France.
Match delayed
"A few foolish people have thought it fit to boo the Marseillaise. It's unacceptable and intolerable. I will not tolerate it and I will not accept something that undermines the values of the republic," Mr Chirac said.
"I have asked for the start of the game to be put off and asked the French federation to apologise to France, which has been humiliated by this gesture," Mr Chirac added.
Mr Chirac left the presidential box and the players returned to their dressing rooms while French Football Federation president Claude Simonet asked the crowd to stop booing or the game would not start.
National shock
Mr Simonet addressed the crowd with a microphone saying, "the French Federation wishes to apologise because the Marseillaise was booed".
"It's our national anthem and everybody must respect it. The game will only start when tranquillity returns," he added.
Francois Nicolai, the president of the Bastia club, also apologised to Mr Chirac, who eventually returned to his seat to watch the game.
Corsica has long been demanding greater autonomy from Paris.
The Marseillaise was booed during a friendly match between France and Algeria on 6 October, causing shock throughout France.
Saturday's incident comes at a particularly sensitive time for Mr Chirac - just a week after he defeated far-right leader Jean Marie Le Pen in the presidential election.
Lorient went on to win the game 1-0.