The first train left the Chhatrapati Shivaji Maharaj Terminus (CSMT) for Kalyan at 7.26 am, an official said.
"The first special train for Kalyan left CSMT at 7.26 am and the second one at 7.44 am," said Sunil Udasi, chief PRO of the CR.
He said services on other sections like Kalyan to Karjat, Kalyan to Titwala and Thana to Kalyan were also operational.
Udasi said since there is still water-logging at Kurla, it may take some more time for the Harbour line trains to get back on track. This line is also operated by the CR.
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"Stranded trains are being cleared first and then CSMT to Thane traffic will resume," the official said.
Services on the suburban corridor of the Western Railway (WR) are also back on track. Trains on this section resumed around midnight last night and more services were started around 7 am.
"Trains running normal over all suburban lines of western Railway @RailMinIndia @sureshpprabhu," Western Railway tweeted.
Speed restriction has been imposed at Matunga Road station from the safety point of view, it said.
Let up in rains last night brought some relief.
The suburban train network, which carries over 65 lakh passengers a day, is the lifeline of the financial capital and yesterday's rain-enforced disruptions caused severe inconvenience to commuters.
Torrential rains pounded the metropolis throughout the day yesterday. The city gauged a whopping 298 mm of rainfall, the highest in a day in August since 1997.
The incessant downpour threw life out of gear and paralysed road, rail and air traffic.