The officer who made the stop reported McDonald to superiors, Ayers said.
Ayers said a criminal investigation has begun and will be directed by the district attorney's office.
The department took swift action, firing the master police officer the very next day. Police said the video is "disturbing and speaks for itself".
By the time McDonald arrived at the scene, the suspect was on the ground and was no longer resisting, Ayers said, noting that no use of force was necessary.
The incident occurred in daylight at a busy intersection. The department says both men are now under criminal investigation.
Bongiovanni appears to be holding a weapon while facing the driver.
"He refused, grabbed his phone and literally started to scream, 'Help me, ' in the phone", 19-year police veteran Bongiavonni wrote in a report.
"This incident - this type of force and this action - was uncalled for", the police chief said. "Situations like this one only makes things worse".
The original video, posted on the Black Lives Matter of Greater Atlanta Facebook page on Wednesday, shows McDonald struggling with a black handcuffed suspect in the middle of a street in the Lawrenceville area as he screams something incoherently. "I'm glad that the second video was forwarded to us".
"With the particular police officer before and he charged me with the same charges as he charged me with yesterday".
Porter said Friday that he's known Bongiovanni since his rookie year at the police academy.
Bongiovanni had arrested Hollins before, according to Ayers. In this video, Bongiovanni can be seen approaching Hollins, who is still inside the vehicle. As he got out of the vehicle, Hollins hit the gear shift and the auto began to roll, forcing McDonald to chase the vehicle, jump inside and pull the emergency brake. Video footage that has since gone viral on Twitter and other social media sites indeed shows a man getting out of his seat with his arms raised, and the officer who pulled him over punching him hard.
"In my previous encounter he reached for a loaded firearm that was under his seat", he wrote in his report. Video surveillance showed the deputy had "forced the arrestee face-first into a brick wall, slammed the arrestee's head into the wall and then punched the arrestee in the back of the head with a closed fist". Bongiovanni asked Hollins to get out of the auto and he resisted, the report said.
Bongiovanni said he deployed his Taser on Hollins multiple times and placed him on the ground. When Hollins tried to get up, Bongiovanni used the stun gun on him again and was then able to handcuff him, it adds.
Hollins, 21, was seen in his booking photo with a bloodied nose and lips.
Both officers did not respond immediately to CNN requests for comment.