Les Bleus opened the scoring through midfielder Eduardo Camavinga but were pegged back in the 24th minute by Omri Gandelman.
Christopher Nkunku scored France's winner just four minutes later thanks to brilliant work by both himself and Camavinga, who combined with the Chelsea forward near the penalty area.
The result leaves France in second place with six points from three games in their four-team Nations League A group, one points behind Italy.
Meanwhile, Israel are six points below France in last place with no points from three matches and would be relegated to League B if they were to remain where they are after another three games.
Israeli goalkeeper Omri Glazer will be disappointed that he was unable to save Camavinga's strike given the Real Madrid midfielder's effort from outside the box on the left was rather tame, but Glazer somehow fumbled his save and allowed the ball to trickle over the line.
Israel's equaliser was well taken by Gandelman, who drifted towards the penalty spot and headed home Oscar Gloukh's cross, but William Saliba and Theo Hernandez will feel they could have done more to prevent Gandelman from having so much time and space in the box.
Camavinga drifted infield from the right of the pitch in the 28th minute and beat two Israeli opponents before passing to Nkunku, who held the ball up with his back to goal near the edge of the penalty area and rolled the ball past defender Ilay Feingold before finishing from the left of six-yard box.
Matteo Guendouzi scored a third in the 87th minute when Theo Hernandez brought the ball from his own half towards the box and combined with Bradley Barcola, before the AC Milan left-back squared a pass to an onrushing Guendouzi, who struck into the bottom-left corner from the edge of the box.
There was still time for a fourth when Barcola struck into the top-right corner from inside the inside of the box on the left after good work from Ousmane Dembele, Randal Kolo Muani and Guendouzi.
ISRAEL VS. FRANCE HIGHLIGHTS
7th min: Israel 0-1 France (Eduardo Camavinga)
Eduardo Camavinga scores in the seventh minute after his strike from distance on the left of the box was somehow spilled into the net by goalkeeper Omri Glazer.
A howler from Glazer!
24th min: Israel 1-1 France (Omri Gandelman)
A cross floats into the penalty area from the left and Omri Gandelman ghosts between William Saliba and Theo Hernandez before guiding his header from the penalty spot past Mike Maignan into the bottom-right corner.
Poor defending from France!
28th min: Israel 1-2 France (Christopher Nkunku)
Camavinga dances past two opponents and drive infield from the right before finding Christopher Nkunku on the edge of the penalty area, and the Chelsea forward finishes from the left of the six-yard box after rolling the ball past centre-back Ilay Feingold.
An exceptional assist and an exceptional goal!
87th min: Israel 1-3 France (Matteo Guendouzi)
Matteo Guendouzi scores a third for France in the 87th minute thanks to good work from Theo Hernandez and Bradley Barcola, with the former squaring a pass to Guendouzi, who strikes into the bottom-left corner from the edge of the box.
That's surely all three points for France?
89th min: Israel 1-4 France (Bradley Barcola)
Ousmane Dembele plays a ball infield from the right at Randal Kolo Muani, who allows the ball to roll between his legs towards Guendouzi before the Lazio midfielder assists Bradley Barcola, who finishes into the top-right corner from inside the box.
There's no doubt about the result now!
MAN OF THE MATCH - EDUARDO CAMAVINGA
Eduardo Camavinga undoubtedly benefitted from a goalkeeping error when he scored the opening goal of the match, but the Frenchman was integral to France's performance.
The Real Madrid midfielder was also heavily involved in Les Bleus' second goal, dancing past two opposition players before finding Nkunku with a deft pass behind Israel's midfield.
Camavinga also won seven of his 12 ground duels, won all five of his tackles and completed 54 of his 60 passes.
ISRAEL VS. FRANCE MATCH STATS
Possession: Israel 32%-68% France
Shots: Israel 1-15 France
Shots on target: Israel 1-5 France
Corners: Israel 0-9 France
Fouls: Israel 8-11 France
BEST STATS
WHAT NEXT?
Israel will take on Italy in their second Nations League game of the October international break on October 14, before they play France once again in the middle of November.
As for Les Bleus, they will face Belgium on Monday, and are set to host Israel before travelling to take on Italy in the November international break.