Both the deceased identified as Shashikant Dhamankar (50) and Deepak Patel, hailing from Mumbai, were crushed under the landslide debris that came down to hit their car.
The three injured, reportedly all women, are being treated at Lokmanya hospital in Pimpri Chinchwad area near Pune, police said.
The mishap occurred at the mouth of the Adoshi tunnel near Khopoli bringing the heavy vehicular traffic to a grinding halt.
Maharashtra Public Works Development (PWD) minister Eknath Shinde who visited the spot said the rescue operation to clear the debris and restart the traffic, though hampered by rains and fog, was going on a war footing and normalization on the route was expected by late evening.
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"We are taking necessary measures to prevent recurrence of such incidents during the monsoon", he added.
"Compensation of Rs 4 lakh each will be given to the the kin of the deceased", Shinde was quoted as saying in an official release.
This is the second landslide in the current monsoon season on the expressway. The earlier one, however, had not caused any casualties.