The university in north-east France's biggest city announced its decision in a Twitter post and the faculty of medicine's dean, Didier Gosset, confirmed it to the AFP news agency on Sunday.
"It has to be said that we teach medicine based on proof - we insist on absolute scientific rigour - and it has to be said that homeopathy has not evolved in the same direction, that it is a doctrine that has remained on the margins of the scientific movement, that studies on homeopathy are rare, that they are not very substantial," he explained. "Continuing to teach it would be to endorse it."
Homeopathy, which was created in 1796 by German physician Samuel Hahnemann, is based on the idea that like cures like, which holds that symptoms that cause a disease can be used to cure it.
Practitioners administer medicines produced by dilution, usually to the point that no molecules of the original substance remain.
Open letter from doctors
The French are among the world's largest consumers of homeopathic medicines and can claim reimbursement of payment for treatment from the social security system.
A group of doctors challenged its official recognition in an open letter in Le Figaro newspaper in March.
They dubbed practitioners of homeopathy and other alternative medicines "charlatans", pointing to a 2017 report by the European Academies Science Advisory Council "confirming the absence of proof of homeopathy's efficacy".
They called on the French medical council to stop accepting practitioners as doctors and on the social security system to stop paying for it.
Other doctors made a formal complaint to the medical council against the signatories.
France's health ministry asked the national health authority to draw up a report on whether homeopathy works and should be subsidised.
The report is due to be delivered in February.