Riders will have to eat the cost for the three days of rides they lost to the storm, the MTA said.
Many subway lines are still partly or fully suspended after Hurricane Sandy.
Subway service is gradually resuming in Lower Manhattan.
The MTA is also close to restoring service on the 4/5 and F lines in Lower Manhattan.
Limited service started Thursday morning with long lines of people waiting for packed buses.
The MTA will restore limited subway lines after Hurricane Sandy and will suspend fares through Friday.
The authority is considering getting some trains at dry stations moving Wednesday.
Mayor Bloomberg said subway service will be shut down for the rest of the week after Hurricane Sandy.
Chairman Joseph Lhota said the MTA has never "faced a disaster as devastating" as the one left by Sandy.
Most of the FDR Drive was also closed Monday because of the storm.
Low-lying areas including Red Hook, Battery Park, and Far Rockaway, were flooded Monday.
The MTA's East Side Access project is expected to be completed in 2019.
James Neverson, 63, was on his way to work when the car hit him Tuesday, officials said.
The MTA is still investigating why the blast rained debris on Second Avenue and 72nd Street.
Firefighters rushed to Second Avenue and E. 72nd Street after a big blast shook the area on Tuesday.
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