The mourners carried the casket of the Islamic Revolution Guard Corps (IRGC) officer, Saeed Abyar, in the shrine of Hazrat Roghayeh, the daughter of the third Shia Imam, Hussein ibn Ali.
An unknown number of people were also killed in the Israeli raid, according to Syrian state media.
Iranian military advisors are invited by the Syrian government to help Damascus fight the remnants of militant groups and their sleeper cells.
Israel occasionally targets Iranian and Syrian forces inside Syria to reverse the gains achieved in their fight against foreign-backed militants.
An Israeli attack on April 1 demolished Iran’s diplomatic compound in Damascus, where two senior IRGC generals and five other officers were killed.
The deadly raid led to a massive retaliatory missile and drone attack by Iran against Israel on April 13.
