The ceremony was a subdued one in the capital, Lome.
About 200 guests were present. They all wore face masks and practiced social distancing.
According to the RFI, only government officials and diplomats attended the ceremony. The country’s borders are closed due to the coronavirus pandemic so no other persons could be invited.
The ceremony was televised. It lasted for a little over 80 minutes, without the usual pomp and ceremony.
Gnassingbe, 53, won by a landslide in February, extending his 15-year reign by another five years.
However, the opposition leader Agbéyomé Kodjo has rejected the results citing fraud. The president's office denies allegations of widespread fraud.
Faure Gnassingbé has led since 2005 following the death of his father Gnassingbé Eyadema, who ruled for 38 years.
President of the Constitutional Court Abdou Assouma, who was present, warned against any challenge to the election results, according to RFI.
The inauguration went ahead despite measures to contain the coronavirus pandemic in Togo.
The West African country has recorded 123 cases and nine deaths, according to the Africa Centre for Disease Control and Prevention.