Abbas asked Prime Minister Rami Hamdallah to remain in the position until a successor is appointed, an Abbas spokesman told Ma'an News Agency.
The move came after the two met in Ramallah.
Hamdallah, the former president of Al-Najah University in Nablus, announced he was stepping down from the position Thursday.
Attempts by Abbas to dissuade him from the move failed.
Hamdallah's decision appears to stem from a power struggle with Abbas deputies Mohamed Mustafa and Ziad Abu-Amr, as well as the refusal by Abbas to grant him more authority, the Israeli newspaper Yedioth Ahronoth reported Sunday.
"Hamdallah discovered that the Palestinian Authority president wants him to serve as a yes-man with no powers," a source told The Jerusalem Post.
Hamdallah was appointed prime minister June 2. Days after his appointment, a new government was sworn in, but Hamdallah made it clear he would step aside in the summer if the formation of a national unity government occurs between Fatah and Hamas, Ma'an said