The Lady Leyla container vessel docked at Ashdod port in the afternoon after departing on Friday, an AFP journalist reported.
Its contents were to be unloaded, inspected and sent on to the Hamas-run Gaza Strip, hit by three wars with Israel since 2008 and under an Israeli blockade.
The Panama-flagged ship was carrying 11,000 tonnes of supplies including food packages, flour, rice, sugar and toys, the Turkish state-run Anadolu news agency reported.
A compromise was eventually reached allowing Turkey to send aid through Ashdod rather than directly to the Palestinian enclave.
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Israel says the blockade is necessary to prevent Islamist movement Hamas from receiving materials that could be used for military purposes, but UN officials have called for it to be lifted, citing deteriorating conditions in the territory.
Turkey's ruling Islamic-rooted AKP party has friendly ties with Gaza's Hamas rulers, and President Recep Tayyip Erdogan has been a vocal supporter of the Palestinian cause.
Under the reconciliation deal, Israel will pay USD 20 million in compensation to the families of those killed.
Prime Minister Benjamin Netanyahu has promoted the economic benefits of restoring ties, with talk of building a pipeline to Turkey to export Israeli gas, and the need to find allies in the turbulent Middle East.
The deal received a mixed response in Israel.
There were allegations that it does not do enough to push for the return of four Israelis missing in Gaza - two soldiers who have been declared dead and two civilians believed to be alive and held by Hamas.