The photograph of the 21-years-old Palestinian medic shot dead by an Israeli soldier on June 1 was brandished by dozens of protesters at the rally to the chants of "Israel murderer, Macron accomplice".
"We are scandalised by Israel's war crimes, the latest of which is firing on civilians in Gaza with explosive ammunition," said protesters who are members of the France Palestine Solidarity Association one of the organisers of the rally.
The protest was initially set to take place in front of the Grand Palais exhibition hall where Macron and Netanyahu were scheduled to inaugurate the joint initiative.
However, police denied the organisers the authorisation to do so, and shut down the two nearest metro stations and bridges at the time the rally was scheduled to start forcing protesters to gather on the opposite bank of the Seine river.
The demonstration was largely peaceful although a small scuffle with police resulted in at least one demonstrator being detained.
On Monday, three of France's top journalist unions also protested Netanyahu's visit in a joint statement, stating that Macron receiving Netanyahu at this time was "unbearable".
The document denounces the killing of civilians in Gaza and the particular targeting of journalists and asks how it is not "inconceivable that the prime minister's visit goes on as if nothing had happened, while a number of NGOs and legal experts are talking about war crimes".
Anger against Israel's policies has been running high in France as a poll carried out in May 2018 found that 57 percent of French people have a "bad or very bad" image of Israel, 73 percent believe Israel bears "a heavy responsibility for the absence of negotiation with Palestinians" and 57 percent believe that "Israel is a threat to regional stability".