The average cost per ton for commcommercial HVAC systems can vary greatly depending on the size of the system, the complexity of the installation, and the type of system being installed. Generally speaking, the average cost per ton for a commercial HVAC system is around $2,000 to $3,000. This cost can be higher or lower depending on the complexity of the installation and the type of system being installed. For example, a more complex system with multiple zones or an advanced control system can cost more than a basic system. Additionally, the type of system being installed can also affect the cost. A packaged system, for example, may cost more than a split system. Ultimately, the average cost per ton for commcommercial HVAC systems can vary greatly depending on the complexity of the installation and the type of system being installed.