Andre Muller, 40, of Manhattan was charge with assault and criminal possession of a weapon.
Isayah Muller -- who led Truman HS to the city championship last fall -- had attended the ceremony with his dad, mom and girlfriend at Lehman College and then went to retrieve their car.
The case is expected to be presented to a grand jury as early as today.
As they headed to a City Island restaurant afterward Andre noticed his son's graduation present of cologne was missing, turned the car around and returned to the garage, cops and family said.
When they arrived at the lot on Jerome Avenue and E. 196th Street around 4 p.m. the father and son began fighting with the workers, cops said.
During the struggle Isayah, 19, was knifed in the chest.
Sources said the father accused parking the lot attendant of stealing the $200 bottle of cologne.
Isayah and his dad rushed back to the car and Andre sped to a medical clinic about 10 blocks away. Isayah was then taken to St. Barnabas Hospital, where he died.
His dad and the attendants were taken to the 52nd Precinct station house. A police source said cops are investigating the possibility the attendants "acted in self defense."
Isayah, who was set to attend Nassau Community College, had a whopping 295 rushing yards and two touchdowns in the title game.
"The kid had all the intangibles that makes football players great," his coach, John-James Shepherd, told The Post.
"He was as loyal a teammate as anyone could ask for and he was as good of a kid that anyone could hope to come across.
"I'm in a state of disbelief. I was hugging this kid at his graduation this morning."
His devastated grandmother, Myrna Valentine, said: "They just took my heart. They broke it into a million pieces."
