The suspects have been identified as 35-year-old Allen Williams and 33-year-old Roberto Grant, both of Brooklyn.
They were apprehended during a car stop in front of 34 East 12th Street at 6:30 a.m. on Friday.
Authorities have said 5 suspects entered the Cartier store at the corner of Fifth Avenue and 52nd Street last Sunday and smashed open a glass display case with a hammer.
Police said they made off with 16 wrist watches worth more than $700,000.
NYPD Commissioner William Bratton says both of the suspects arrested on Friday have extensive criminal records.
They are being investigated as part of a pattern of six similar smash and grab robberies at jewelry stores in Manhattan and Queens last year.
Investigators were reviewing security video to try to identify all of the suspects, but so far, none of the surveillance has been released.
Authorities said some wore masks and all had gloves on.
The heist occurred as football fans were flocking midtown Manhattan for festivities related to the Super Bowl in New Jersey on Sunday.