The men, a 29-year-old from Kenthurst and 24-year-old from Castle Hill, will face Blacktown Local Court on Thursday, a day after they were arrested by heavily armed police at two properties in Sydney's northwest.
Senior police allege the duo and a third unknown person took 85-year-old widower Chris Baghsarian from his North Ryde house about 11 days ago in a case of mistaken identity.
Authorities have confirmed human remains found near a golf club on Sydney's northwest outskirts on Tuesday are his.
They believe Mr Baghsarian was killed at a makeshift stronghold in the semi-rural Sydney suburb of Dural before his body was dumped hours later.
"It's somebody's worst nightmare, right?" Detective Acting Superintendent Andrew Marks said.
"These people need to be held to account for that, and that's why we are bringing these people before the courts."
Vehicles, electronics and clothing relevant to the investigation were seized during the search warrants at Kenthurst, Castle Hill and Lake Macquarie.
Police are searching for the third alleged offender with the belief that more were likely involved in the incident.Â
Authorities believe the intended target for the abduction was a relative of underworld-linked Sydney businessman Dimitri Stepanyan, who lived on the same street as Mr Baghsarian.
Det Act Supt Marks suspected the intended target was to be kidnapped in hope of a ransom fee being paid, and confirmed reports the figure demanded was $50 million.
Mr Baghsarian's family, who described the harrowing ordeal of the kidnapping as a "nightmare", expressed relief the alleged offenders had been caught.
They have asked for privacy, as they come to grips with the death of their devoted father, brother, uncle and grandfather "who would never hurt a fly".
24°C