Midfielder Florent Malouda scored the winner when he fired under the crossbar from a Djibril Cisse cross just before halftime in one of the few highlights of a close, tactical match against opponents also on their way to the finals in Germany.
The 33-year-old Zidane, who will retire after the World Cup, was playing for the last time in his glittering career at the Stade de France, where he scored twice in France's 3-0 defeat of Brazil in the 1998 World Cup final.
The three-times World Player of the Year could only offer a below-par performance and was substituted early in the second half under deafening cheers from the crowd.
"I have plenty of memories in this stadium," said Zidane, who scored in the inaugural game at the showcase arena on the outskirts of Paris, a 1-0 win over Spain in January 1998.
"Everything has to end. I'll come back, as a spectator. Now we all have to focus on the two matches we have left before the World Cup. It was important to start with a win today."
France will play two more friendlies against Denmark and China before starting their World Cup Group G campaign against Switzerland on June 13 in Stuttgart. They also face South Korea and Togo in the group phase of the tournament.
"We were not as fresh as they were physically and we suffered," said Domenech.
"I had expected that. We worked hard tonight and this victory will give us some energy for the hard work we've got ahead of us."
FEW CHANCES
Mexico, who have now lost five times and drawn once in six meetings with France, meet Portugal, Iran and Angola in Group D in the World Cup which kicks off on June 9.
France controlled the match from kickoff but created few chances until midfielder Patrick Vieira hit the crossbar from 20 metres on 15 minutes.
Mexico showed little initiative before the break but warned they could be dangerous when a header by defender and captain Rafael Marquez from a free kick flew just over the bar in the 34th
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The Stade de France woke up in the 63rd minute with a fluent move sparked by Malouda which ended with a David Trezeguet header that failed to surprise Mexico goalkeeper Oswaldo Sanchez.
Midfielder Franck Ribery, hailed by many as the next Zidane, came on for the last 15 minutes to win his first cap and looked promising.
The World Cup should provide the gifted 23-year-old with further opportunities to prove his worth.