Luke Briggs was arrested in a convenience store car park at Hoppers Crossing, in Melbourne's southwest, in July 2024.
The 35-year-old became unresponsive at the scene and died eight days later at Royal Melbourne Hospital.
The two male Victoria Police officers involved, a constable, 29 and sergeant, 45, were suspended after the incident.
They were charged on Thursday and will face Melbourne Magistrates Court on Friday.
Victoria Police Deputy Commissioner Wendy Steendam said she was aware news of the charges would be concerning and difficult for many in the community.
"I want to reassure them that Victoria Police does not shy away from taking action to uphold community trust and confidence in our organisation," she said.
It was vital that such incidents were investigated thoroughly regardless of an officer's rank, adding the overwhelming majority of police did the right thing, Ms Steendam said.
"Our thoughts today are also with the Briggs family and we will ensure they continue to have a range of support services in place as the matter progresses," she said.
The incident was investigated by the homicide squad and overseen by Professional Standards Command, an internal police branch that examines officers' conduct.
Mr Briggs' family said he died in an intensive care unit wearing his favourite Bunnings jumper, beer by his side and surrounded by his loved ones.
"In his final hours, we shared stories and reminded Luke how much we loved him while his favourite songs played in the background," they said in a statement at the time.
"We will miss you, Luke. We don't know how we can go on without you."
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