Israel does not recognise the slaughter of Armenians at the hands of the Ottoman forces between 1915 and 1917 as "genocide".
"For the first time, an Israeli president has marked the mass massacre of the Armenian people with the Armenian community of Israel," the presidency said in a statement.
Armenia's honorary consul in Israel, Tsolag Momjian, welcomed the participation of Israeli officials in ceremonies marking the massacre, after two lawmakers travelled to Yerevan to take part in commemorations.
But the representative of the Armenian Patriarch in Israel, Aris Shirvanian, denounced Israel for not having yet referred to the mass murder of Armenians as "genocide".
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Israeli lawmakers have in the past debated recognising the Ottoman era massacre of Armenians as "genocide", but only at a time when the Jewish state's relations with Turkey were strained.
The Armenians say up to 1.5 million people were killed during World War I as the Ottoman empire was falling apart, a claim supported by several other countries.
But Turkey strongly denies the genocide allegations, and argues that 300,000 to 500,000 Armenians and at least as many Turks died in the civil strife when Armenians rose up against their Ottoman rulers and sided with invading Russian troops.
Hundreds of thousands of Armenians commemorated the massacres on Friday as April 24 is accepted as the date in 1915 when Ottoman Turkish mass killings of Armenians began.
In attendance at commemorations in Yerevan were Russian President Vladimir Putin and French counterpart Francois Hollande, who called on Turkey to recognise the genocide.