Gov. Cuomo vetoed bipartisan legislation that would have provided fare relief to commuters who have to take two buses and a train to reach their destination.

The measure, which overwhelmingly passed the state Legislature in June, would have allowed riders on some routes to get two free transfers instead of one within two hours.

MetroCards now allow one free transfer between a subway and a bus or between two buses during a two-hour period.

As part of their commute, most of these riders have to take two buses before reaching the subway and are paying two fares, said the bill’s sponsors, Assemblyman Jeff Dinowitz (D-Bronx) and Sen. Martin Golden (R-Brooklyn).

Cuomo hung his veto on opposition from the Metropolitan Transportation Authority, which claimed it would cost a bundle to provide the extra free transfer for up to 50,000 riders.

“The MTA estimates it would cost approximately $40 million annually to provide a second free transfer, yet the bill does not provide any funding to account for this expense,” Cuomo said in his veto message.

“Such funding decisions should be addressed in the context of the state budget negotiations,” Cuomo added.

In its memo opposing the bill, the MTA said adding a second free transfer would also present difficult technical issues.

Transit officials say a simple solution already exists: Commuters can buy an unlimited-ride Metro­Card, which allows for multiple free transfers.

Cuomo echoed that point.

“The MTA also offers an unlimited-ride MetroCard for purchase,” Cuomo said. “Multiple free transfers can be made with these weekly and monthly unlimited-ride cards, and more than half of the MTA customers already use these unlimited-ride cards.”

But Dinowitz says Cuomo and the MTA are leaving riders in the lurch — especially those who cannot afford the monthly outlay for an unlimited-ride card.

“The MTA is not known for putting out accurate numbers,” he said. “It’s just not fair for people who, through no fault of their own, have to take three rides and are in a two-fare zone.”