The government's comes into effect from today.
A group of private toll contractors had challenged it, disputing the government's compensation package of Rs 306 crore. They claimed dues of Rs 3,000 crore.
The petitioners had asked for an interim relief by way of a stay on the government's decision but a division bench headed by Justice Naresh Patil did not grant the stay.
There are 166 toll roads in the state.
Earlier this month, the state government decided to close down 34 booths on roads under the control of PWD and 10 roads under Maharashtra State Road Development Corporation. These booths are in Nashik, Amaravati, Nagpur, Jalgaon, Dhule, Aurangabad, Pune, Sangli, Solapur, Satara and Raigad districts.
The booth contractors contend the government's decision is arbitrary and discriminatory and they are yet to recover the money invested in road construction.