The bus was heading for Pune from Trimbakeshwar in Nashik district, Narayangaon police said.
The accident spot is 77 km away from Pune.
"It seems the bus driver could not see the tempo due to heavy rain," a police officer said.
The accident took place at around 1.45 am when the driver of the tempo, which was carrying onions, had halted by the roadside to change a flat tyre.
"Identities of the deceased are yet to be ascertained," the officer added.
Injured passengers were being treated at nearby hospitals.