Vimal Pandey, a native of Allahabad, was arrested from Delhi in the wee hours, a senior official said.
Police is conducting raids in Rajasthan and Haryana to nab his associates, of which two have been identified as Deepak and Vishal, he said.
Two of the suspects in the case were arrested in Rajasthan in connection with robbery and murder, the official added.
The incident took place on Sunday morning when four assailants allegedly shot dead cashier Manmohan (60) and security guard Mahipal (50) at their rented accommodation near the toll collection centre in a robbery bid and fled with a laptop bag.
It also emerged that they had rented a room by submitting fake documents, following which the landlord of the house was booked, police said.