Defending champion Martin Kaymer is the nearest challenger on nine under par after the 25 year old German added a 67 to his opening 66 at Le Golf National near Paris.
Last year Kaymer beat Lee Westwood in a play-off on the course, then went to The Barclays Scottish Open at Loch Lomond and won there as well.
But just a few weeks later he broke three toes in a go-kart crash and was forced out of the game for two months.
Currently sixth in the race for places in Colin Montgomerie's Ryder Cup side for The Celtic Manor Resort in October Kaymer said: "I went go-karting again earlier this year, but there will definitely be no more before The Ryder Cup."
Both he and Cañizares, son of 1989 Ryder Cup hero José Maria, had their rounds interrupted for nearly 2 1/2 hours by a thunderstorm.
At that stage they were two behind Dutchman Robert-Jan Derksen, but Cañizares then had four birdies in his last five holes for a second 66 in a row and Kaymer birdied the tenth, 14th and 17th.
"My dad is coming tomorrow, so I'm really looking forward to the weekend," added World Number 11 Kaymer.
Cañizares, whose one previous victory came in Russia four years ago, had to return to The Qualifying School last November, but fellow graduates Simon Khan and Fredrik Andersson Hed have already lifted trophies and the 27 year old from Madrid hopes to do the same on Sunday.
"I was a little negative in my play last year, I wasn't into it very much and had a couple of problems, personal problems," said Cañizares.
"But this year, I came out, I got my card again, so it was like a new start and I knew what I lost and I learned to appreciate it a little more, this game, and try to have fun and try and enjoy it.
"I played with him [Khan] the first three days I think, and he played great at Q-School and I thought he was going to be great this year.
"He started a little slow but you never know in this game, and he won the biggest tournament of the year and very happy for him."
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