The Senegalese Football Federation confirmed on Thursday evening that the 30-year-old had been released from Patrick Vieira’s squad and returned to the Ligue 1 side.
Niakhate has been an important figure for the French club this season and has rarely been rested despite their involvement in multiple competitions.
The centre-back has already made eight appearances across all competitions, including three UEFA Champions League qualifiers.
The nature of his injury has not been disclosed, but the defender underwent an MRI scan in Marseille on Monday.
Following the examination, the decision was taken to send Niakhate back to Lyon for further assessment and treatment.
He will consequently miss Senegal’s upcoming international fixture against Comoros on October 4.