Israel's UN mission said ambassador Ron Prosor's had gone to the event through a "misunderstanding."
Le Pen said however she hoped his presence had proved that the National Front party had turned the page on incendiary remarks made by her father Jean-Marie Le Pen about Nazi gas chambers.
About 30 people were invited to the meeting. Among diplomats, only Prosor, the deputy ambassador for Japan, Kazuo Kodama, the Trinidad and Tobago ambassador Rodney Charles, Uruguay's envoy Jose Luis Cancela and Armenia's Garen Nazarian attended.
The Israeli ambassador left after less than 20 minutes, before the formal lunch started.
"The ambassador was there through a misunderstanding," said Israeli mission spokeswoman Karean Peretz, without explaining.
On leaving, Prosor said diplomatically "we flourish on the diversity of ideas. We talked about Europe, about other issues and I enjoyed the conversation very much."
Le Pen is credited with 17-19 percent support in French opinion polls and is on the US tour seeking to bolster her image. She denies her party is anti-immigrant.
However many people still associate the National Front with 1987 comments made by her father Jean-Marie Le Pen that World War II Nazi death camps were a "detail of history." He repeated the comments and was convicted of inciting racial hatred.
"This misunderstanding has lasted years and has been used as a basis for a caricature which has damaged our movement," she told journalists after the lunch.
The meeting had sent a "signal... that the page has turned" on "past misunderstandings between French Jews and the National Front."
"I think this lifts an accusation," she added.
The French politician said it was the first time she had met with an Israeli official, and said she was ready to travel to Israel if she received a formal invitation.
Le Pen said she and Prosor discussed the eurozone crisis and Arab Spring protests in the Middle East.
On Friday, Le Pen said she may meet with Occupy Wall Street protesters in Manhattan. She says she shares their anti-establishment message.
In Washington on Wednesday, Le Pen met with Republican Representatives Joe Walsh and Ron Paul, a presidential candidate, before heading to the headquarters of the International Monetary Fund, which she accused of "starving the people."
Le Pen said the French government had made it clear it did not want her to go on the tour.
"The French government is very upset with my presence here and is seeking to minimize the impact of my visit by any means possible," she said on Wednesday.