He was joined by his family and a few government officials.
The presidency had announced that Buhari will conduct the prayers at home.
Garba Shehu, the Presidential spokesman, said the decision was in respect to the lockdown measures in the Federal Capital Territory, Abuja.
It was also in accordance with the directive of the Sultan of Sokoto and President General of the Jama’atu Nasril Islam (JNI), Sa’ad Abubakar III.
Buhari also obeyed the protocol against mass gathering issued by the Presidential Task Force on COVID-19.
For the first time since he assumed power in 2015, the president will not receive guests during the Eid celebration.