The first train left Churchgate in south Mumbai for Virar at 11:58 pm, the Western Railway tweeted. "Evacuation of all stranded passengers is priority and trains will be run throughout the night, if required," it said.
Mumbai's suburban train network, which carries over 65 lakh passengers a day, is the lifeline of the financial capital and stopping the services had led to inconvenience to many office-goers who had braved the heavy rains to make it to their offices.
Heavy rains in Mumbai have caused traffic jams in major roads all across the city.
The Central Railway, which operates trains from the Chhtrapati Shivaji Maharaj Terminus, tweeted around 11:30 pm that services on the Thane-Kalyan line, which is a section on the main line, had resumed.
Every minute of Mumbai's day on Tuesday was nightmarish after the city received over 10 times the rain that it gets during the monsoon. Four inches of rain were recorded in just four hours the morning - and by then, the financial capital was gridlocked with traffic. By the time officials began urging people not to leave home unless absolutely necessary, cars were bobbing along in water, trains were running late with tracks submerged, and key highways and roads were choked.
Heavy rain has been forecast for today as well, and schools and colleges have been told not to open.