The prayers were held at his residence with members of the first family in attendance.
His wife, Aisha, son, Yusuf, and other children were sighted attending the prayer session with Buhari.
The President had earlier announced on Friday that he would mark the occasion at home in compliance with the measures put in place in the Federal Capital Territory to guard against the spread of the raging COVID-19.
He had advised other Muslims to do the same by staying at home to observe social distancing.
The President had also barred any form of Sallah homage to the State House by government officials and other groups.
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