The Bangalore police arrested the accused - Prince John, aka Johnson, 31 - on Sunday. He has been remanded in 14 days of judicial custody by a local court.
"The accused raped the victim on May 13 in Bangalore. He had threatened her with dire consequences if she went to the police. Later, the victim fled to Mumbai and lodged a complaint with the police there.
The case was transferred to us and we arrested Prince John," said Bangalore rural superintendent of police D. Prakash.
According to the police, Prince John, who is in Bangalore on a student visit, befriended the victim's aunt a few months ago. On May 13, the victim and her aunt visited Prince John at his residence.
"Subsequently, he told his girlfriend (victim's aunt) that he would take her (victim) for an introduction to a friend, who would help her solve a personal crisis. He took the unsuspecting victim to a house where he raped and threatened her," the police added.
The victim is now undergoing treatment at a hospital in Mumbai.
The incident has caused unrest among the North East student community. In April, the death of Manipuri student Richard Loitham and the shoddy investigation by the police in the case had led to a countrywide uproar.
This is not the first time that African students have been nabbed for crime-related activities. Earlier this year, two African students were arrested for fighting in public glare over a girl; another six African students, under the influence of alcohol, had attacked the traffic police.
In Bangalore, nearly 2,000 students from Kenya, Uganda, Tanzania, Congo, South Africa, Nigeria, Ivory Coast, Cameron, and Sudan are studying in various colleges, according to Union of African Communities of Bangalore. Some of them allege harassment by the police for trivial reasons.
"Now, managing both, students from North East and Africa, has become a sensitive issue. But we will allow law to take its own course," the police added.