Health Minister Awa Marie Coll Seck told a news conference the young man had turned up for treatment at a hospital in the Senegalese capital Dakar on Tuesday but concealed that he had had close contact with victims in his home country.
She said Guinean authorities said the student from the Guinean capital Conakry had disappeared three weeks ago while under surveillance for having close contact with Ebola victims.
"The results of tests carried out by the Pasteur Institute in Dakar were positive (for Ebola)," the minister said.
The worst ever outbreak of the deadly virus, first detected in the jungles of south-east Guinea in March, has killed more than 1,550 people. Most of these were in Guinea, Sierra Leone and Liberia, but six people have also died in Nigeria.
Dakar is a regional hub for UN agencies and aid groups serving the Sahel region of West Africa. It also serves as a regional base for many companies, from financial services to banking and tobacco.
In an effort to insulate itself from the worst ever Ebola epidemic, Senegal announced last week it was closing its southern land border with Guinea.