Turkish diplomats and Israeli Foreign Ministry deputy spokesperson Oren Rozenblat were present at the port as the Panama-flagged Lady Leyla docked.
The ship carries 10,000 toys and 10,000 packages of food and aid for children in Gaza.
Five tons of flour and 2,000 tons of rice aid from the Turkish Grain Board, as well as sugar aid from the Turkish Red Crescent, will also be delivered.
The ship set sail on Friday following a reconciliation deal reached between Turkey and Israel on Monday after a six-year hiatus.
Diplomatic ties between the two countries were suspended after Israeli troops stormed the Gaza-bound Mavi Marmara aid ship in international waters in 2010, killing 10 Turkish activists.
In the aftermath of the attack, Turkey demanded a formal apology from Israel, compensation for the families of those killed, and the lifting of Israel’s Gaza blockade.
In 2013, Israeli Prime Minister Benjamin Netanyahu voiced regret for the attack.
On Monday, months of talks between the two countries finally bore fruit, with Turkey announcing that a deal would be signed, normalizing relations with Israel.
Under the deal, in addition to agreeing to Turkey’s humanitarian presence in Gaza, Israel will pay $20 million in compensation to the families of the Mavi Marmara victims.