One accused was arrested from Dhaula Kuan in Delhi and while another was nabbed from Ghaziabad, said UP STF IG Amitabh Yash.
Police have also seized the car and fake number plate used in committing the crime.
He said that CBI had sought the help of the STF in arresting the accused.
The IG said that the accused wanted to loot the Ankit's car but could not do so as a crowd had gathered on hearing the gun-shot. 27-year-old software engineer Ankit was shot dead on April 13, 2015.
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During interrogation, the accused told the police that Pankaj had taken Rs 4 lakh loan from Shashank and then refused to return it. Later, the trio hatched a plan to rob the Ankit's car to recover their loss.
In June last year, Allahabad high court had transferred the case to the CBI after Noida police failed to crack the case even after one year.
The move had come after Ankit's father, Dharamveer Chauhan, filed a criminal writ petition demanding that the probe be handed over to the CBI.
Ankit was murdered on a busy stretch in Noida's Sector-76 when he was returning after meeting his wife Ameesha, who is also a software engineer. The two had been married for just 34 days before his death.
At the time of the murder, Ankit had been with his cousin Gagan when the assailants first overtook his SUV and fired at the windscreen. One of the assailants then got out of the car, shot Ankit in the neck, and sped away. He was taken to Kailash Hospital, but was declared brought dead.