Brendan Gorman, 19, and Codi Fuller, 21, were arrested at properties in western Sydney on Tuesday morning.
It follows the earlier arrests of another four people in relation to the grandfather's death, which police believe was a case of mistaken identity.
Mr Baghsarian was allegedly taken from his North Ryde home in the early hours of February 13, sparking a major search effort during which police urged his kidnappers to release him.
Detective Acting Superintendent Stuart Gordon said on Wednesday the young men arrested had effectively thrown away their lives with no payoff for their alleged crimes.
"We've seen a number of high-profile kidnappings in recent times but what we're seeing is predominantly young males, often teenagers, who are committing the most serious of criminal offences," he told reporters.
"Here are a group of young men who have thrown away the best years of their lives doing something so staggeringly serious for nothing."
Murder carries a life sentence in jail and a kidnapping offence carries a 25-year sentence under NSW laws.
Mr Baghsarian's body was found 11 days after he vanished near a golf club in the semi-rural suburb of Pitt Town in Sydney's north-west.
Police allege the elderly widow was not the intended target of the kidnap-ransom plot.
They suspect the perpetrators aimed to abduct a relative of Sydney businessman Dimitri Stepanyan, who lived on the same street as Mr Baghsarian, in the hopes of receiving $50 million for his return.
His alleged kidnappers Gorman and Fuller were charged with murder and taking or detaining a person in company with the intent to ransom while occasioning actual bodily harm.
Gorman was also charged with failing to comply with a digital evidence access order direction.
Both men appeared in court on Wednesday, where they did not apply for bail.
They are likely to remain in custody until their cases return to court on July 17 with other accused offenders.
A 23-year-old believed to have orchestrated the kidnapping was arrested and charged in March, while another 19-year-old man was charged in April with murder and supplying a firearm used in the kidnapping.
Earlier, two men aged 29 and 24 years old were also charged for their roles in the alleged plot.
Investigators have previously said they believe up to nine people may have been involved.
Police believe Mr Baghsarian was killed at a makeshift stronghold in Dural, on Sydney's northern outskirts, before his body was dumped.
His family described the ordeal as harrowing, remembering him as a devoted father, brother, uncle and grandfather.
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