Netanyahu told Abbas "everyone in Israel was shocked by the reprehensible terrorism against the Dawabsha family" that killed the 18-month-old boy, his office said.
"We must fight terrorism together, regardless of which side it comes from," he added.
Netanyahu further told Abbas he had ordered the Israeli security forces to "use all measures to locate the murderers."
After speaking with Abbas, Netanyahu visited the Israeli hospital where the mother and brother of Ali Saad Dawabsha were being treated for severe burns.
Prior to that, the two spoke had not spoken since June 2014, when Netanyahu asked Abbas for help in ensuring the safe return of three Israeli teens kidnapped by Palestinian militants, who murdered them.