A pharmacy worker recognized him as the man shown in surveillance footage leaving the scene of the most recent shooting, Nov. 16, with a duffel bag, police said.
Another shopkeeper came forward and said Perrone had gone into his store and questioned him about whether he worked alone and when he closed, Police Commissioner Raymond Kelly said.
"It's reasonable to assume he was going to keep doing this, and, by arresting him, we saved lives," Kelly said.
Detectives said they found the duffel bag at his girlfriend's home. Inside, they said, was a sawed-off rifle used in the killings, along with .22-caliber ammunition, black gloves, women's clothing, a bloody knife and a bottle of bleach.
Perrone's fingerprint was lifted from the murder weapon, Kelly said.
Initially, authorities thought the killer might have targeted the Brooklyn shopkeepers, who were from Iran and Egypt, because of their backgrounds. But Kelly said there was no motive he could speak of.
In the most recent killing, Rahmatollah Vahidipour, an Iranian, was shot three times.
After that killing, detectives discovered the same gun was used in the fatal shootings of two other shopkeepers when ballistics matched the .22-caliber shell casings.