The French leader also pledged to fight continued anti-Semitism in his country.
Elie Barnavi, a former Israeli ambassador to France, told AFP news agency: "The presence of Netanyahu makes me a little uneasy". The Jewish community must know that we, the veterans, did not abandon them. "Militant Islam wants to destroy our common civilization".
He remarked that Hollande and his predecessor Nicolas Sarkozy sought to build good ties with the Israeli premier, "but they quickly failed". His last official visit to France was to attend the unity march following the attacks on satirical magazine Charlie Hebdo, police officers, and a kosher supermarket in January 2015.
After meeting with Israeli Prime Minister Benjamin Netanyahu, Macron told the press that Israelis and Palestinians should be able to live in recognized, secure borders. "Out of the ash of destruction, we established the Jewish State". Almost 13,000 Jews were gathered and then deported to Auschwitz concentration camp in Germany in July 1942. The incident is named after the Vélodrome d'Hiver stadium, an indoor cycling track where the victims were temporarily held before deportation. Less than a hundred of those arrested in the raid would survive the Holocaust.
Senator Schumer: Macron 'absolutely right' in equating anti-Zionism with antisemitism
Netanyahu was the first Israeli leader to speak at the annual event in memory of the Vel d'Hiv roundup, which led to criticism by some leftist Jewish French groups, who argued that this event had nothing to do with Israel.
Many politicians in France have acknowledged France's responsibility for the murder of almost a quarter of its Jewish population, including Jaques Chirac who, as president in 1995, said that France "carried out the criminal insanity of the occupier" at Vel d'Hiv.
Macron said that it was France that organized the roundup of the Jews.
"We have a responsibility to realize where and when we have failed", he said. "It seems that the values of the French Revolution - liberty, equality, fraternity - these values were crushed brutally under the boots of antisemitism". And thus 13,152 people of the Jewish faith were dragged from their homes between the 16th and 17th of July 1942 to their death.
The ceremony and Netanyahu's visit comes just days after after renewed tensions in Jerusalem following an attack in which two Israeli policemen were killed.