Still, questions remain over how the state and city will pay for their shares of the plan. Mr. Cuomo has said the state’s share will come from its general fund, and the details will be worked out with legislators when they return for the next session in January.

The agreement between Mr. Cuomo and Mr. de Blasio to fund the plan followed heated debate over whether the city should pay more to the state-run authority. The deal calls for the state to pay $8.3 billion over five years toward the plan and for the city to contribute $2.5 billion over five years, substantially more than its initial commitment of $657 million.

The capital plan now must be approved by the state’s Capital Program Review Board, which includes representatives of the governor, the mayor, the Assembly speaker and the Senate majority leader. The plan calls for new train cars and buses, updated signal systems and work on a new fare payment system. The investment comes as the subway struggles to handle growing ridership and rising delays and overcrowding.

On Wednesday, Mr. de Blasio highlighted $300 million in city projects he said he had worked to secure as part of the funding deal, including $30 million for a new pedestrian pathway connecting the Livonia Avenue and Junius Street stations in Brooklyn and other station improvements. The plan includes $5 million for the Utica Avenue subway study, an idea that has been debated for at least a century in an area of the city that some officials argue needs better transit access.

But the plan includes only $535 million for the second phase of the Second Avenue subway, down from $1.5 billion in the capital proposal from last year. The first phase of the subway line, which will extend the Q line to 96th Street, is expected to open in December 2016.