The incident occurred around 2 p.m. on May 29 in the area of Plymbridge Crescent and Plymbridge Road.
The victim, who was identified by the City of Toronto as Curtis Smith, was working in the area when he was pinned between a garbage truck and a tree.
Smith was rushed to a trauma centre in life-threatening condition.
According to a GoFundMe page set up to help cover funeral expenses, Smith was treated for two broken collar bones, a fractured jaw, 12 broken ribs and two punctured lungs.
A week later, his condition deteriorated and he passed away.
Smith and his partner were expecting a child, the GoFundMe page said, and he had been working a fair amount of overtime in preparation for the new addition to his family.
"Our thoughts are with Mr. Smith's family and his colleagues during this difficult and tragic time,” Toronto Mayor John Tory said in a statement. “The safety of our workers is of the utmost importance and this incident will be thoroughly investigated to make sure we are doing everything we can to protect them."
Smith began working as a waste collector in 2014 and was described by City Manager Chris Murray as a “hard worker and dedicated public servant.”
Flags at City Hall and civic centres will be lowered to half-mast until sunset on the day of the funeral, the city said.
Both Toronto police and the Ministry of Labour are investigating the incident.