The Prophet (may Allah's peace and blessings be upon him) prayed over a grave after he had…

The Prophet (may Allah's peace and blessings be upon him) was created with good manners, such as mercy and compassion. Whenever he missed any of his Companions, he would ask about him and check his condition. He asked about a man, and the Companions told him that he had passed away. So he wished that they would have told him so that he could have prayed over him, for the Prophet's prayer would bring tranquility to the dead and dispel the darkness in which a deceased lies.

As the man was already buried, the Prophet prayed over his grave in the same way he would pray over a dead person who was not yet buried. It should be noted that the Prophet's prayer over the grave does not mean that he stood over it. Rather, he stood next to it while facing it and performed the funeral prayer.