The ceremony was held on Wednesday at the holy shrine of the eighth Shia imam, where the late president was laid to rest last week.
A group of top Iranian officials attended the ceremony as well.
Raisi and his companions, including foreign minister Hossein Amirabdollahian, lost their lives on May 19 when their helicopter crashed in Varzaqan region, in the northwestern province of East Azarbaijan.
The president and his accompanying team were heading to the provincial capital Tabriz from a border area where Raisi and his Azerbaijani counterpart Ilham Aliyev had inaugurated a joint dam project.
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