A married couple from Brooklyn Heights has adopted the 4-month-old kittens, named Arthur and August.
The kittens shut down about six miles of track on August 29 after they were spotted wandering in the subway system.
The New York Police Department sent officers to the scene for crowd control as trains stopped running for about 90 minutes.
Animal Care and Control of NYC says the kittens were sheltered for about two months before they were eligible for adoption.
A spokesman says one was underweight, and both needed to be socialized.
He says they got a lot of inquiries and applications to adopt them, but Katherine and Keith Lubeley really impressed the adoption counselors.