Binyamin Netanyahu has offered good wishes to the world's newest country following its independence on July 9 at midnight.
The Republic of South Sudan was created in 2005 in a peace agreement ending decades of civil war. The Israeli Prime Minister said Israel recognised the new state and added: "We wish it much success."
He also said Israel "would be pleased to co-operate with it in order to ensure its development and its prosperity" and described it as "a peace-seeking country".
There were celebrations in Tel Aviv, where many refugees escaping the conflict in the Darfur region of Sudan now live.
At birth, the new state is one of the poorest in the world, with extremely low rates of life expectancy and high levels of infant mortality.
Israeli humanitarian organisation IsrAID announced that it would send a team to help the fledgling country.