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Faroes defender Suni Olsen contributed to France's victory five minutes later when he deflected a cross from Cisse into his own net.
France were in a class of their own throughout the match against the brave but limited, largely amateur side from the North Atlantic, missing many opportunites before Cisse completed the victory by firing under the crossbar from a fine Sylvain Wiltord pass on 76 minutes.
Raymond Domenech told his players not to get carried away with the victory, though.
"It's only the first stage on the road to qualification. Nothing is done yet and we are still in the same situation as before the tie, we need to win all our matches to finish top of the group."
The best player on the pitch, however, could be missing for the game against Ireland as Cisse sustained a sore ankle in the match.
But Cisse was happy with his performance saying: "It was a great match for me. It's certainly one of my best nights for quite some time. I'm playing pretty well at the moment."
France, with influential playmaker Zinedine Zidane back to help them, now join Ireland and Switzerland at the top of Group Four with 13 points from seven games and next face Ireland in Lansdowne Road on Wednesday in a match that could be decisive in determining who eventually wins the group.