Israel and Lebanon have technically been at war since 1948, and Lebanon boycotts its southern neighbour.
"I love and respect Elie Saab, but is he really happy an Israeli actress wore a dress he designed?" asked Lebanon journalist Heba Bitar on Twitter.
The picture of Gadot has since been removed from Saab's Instagram account.
The image of the Wonder Woman star in a blue sash dress by Saab and was accompanied by a description of the former Israel Defense Forces combat trainer as "flawless".
Saab's Instagram post saw some people share their frustration that a former member of the Israeli army would be promoted by the designer.
Gadot was wearing the dress to the National Board of Review awards in New York, where she and director Patty Jenkins received the Spotlight Award for their work on Wonder Woman.
The deleting of Saab's picture has drawn a mixed reaction on social media. While one user praised the decision to remove the post, another called the whole debacle "shameful".
This is not the first time Gadot has found herself in the middle of controversy due to her nationality.
In 2014 the actress voiced her support of the Israeli armed forces on Facebook during the Gaza War, which left more than 2,100 Palestinians dead. On the Israeli side, 67 soldiers and six civilians were killed. The post was both condemned and condoned in thousands of comments.
In 2017, her superhero blockbuster was banned from Lebanese cinemas, specifically because of her casting as the title character.
However, this ban did not extend to Justice League, which also stars Gadot as Wonder Woman, released later that year.