Ahmed Al Sharaa
El-Sisi also took part in a group photo with leaders and participants attending the summit.
The meeting, held ahead of a summit between the United States and Gulf Arab countries, comes a day after Trump surprisingly announced lifting all sanctions on the Islamist-led government.
The transitional phase will reportedly last for five years.
This surge in violence marks one of the deadliest periods since the onset of the Syrian war in 2011.
In his congratulatory message to Al-Sharaa on social media, Sisi expressed, “[I extend] my wishes for his success in achieving the aspirations of the Syrian people toward greater progress and prosperity.”
Spokesman of the Military Operations Department in Syria announced on Wednesday that Ahmed Al-Sharaa is now carrying out the duties of Syrian presidency, for the transitional phase.