The second suspect was apprehended early Monday in the eastern state of Bihar, where the first suspect was arrested on Saturday.
There are reports the 24-year-old man who was arrested first told investigators a friend was involved in the assault.
Both men were transported to New Delhi, 1,000 kilometres from Bihar following their arrests.
- Nahlah Ayed: Delhi's voices, women and rape in India
The girl was allegedly abducted and then sexually assaulted over a 48-hour period. Doctors at the hospital where she is being treated say she is conscious and in stable condition.
Police say the girl went missing April 15 and was found two days later by neighbours who heard her crying in a locked room in the same New Delhi tenement building where she lives with her family.
The girl was alone when she was found, having been left for dead following the brutal attack, police say.
Child rights activists in India say this is just the latest case in which police failed to act on a report of a missing child. When the parents of the girl went to report that their daughter was missing, police refused to register a complaint, activists say.
For two days, the parents pleaded with police to begin the search for their child, but social activists say officers did not file a report that could get an investigation underway.
Even after police recovered the girl, activists say reaction was true to form: the parents say the police offered the couple 2,000 rupees ($37 Cdn) to keep quiet about what had happened to their daughter.
Since the story became public, hundreds of people have protested in New Delhi, accusing police of failing to act and an ingrained class bias which makes them indifferent toward complaints by the poor and powerless.
The incident came four months after the fatal gang rape of a young woman on a New Delhi bus sparked outrage across India and spurred the government to pass tough laws for crimes against women, including the death penalty for repeat offenders or for sexual assaults that lead to the victim's death.