A native of New York, New York, Novoa attended Fordham Preparatory School and played college baseball for Villanova, where he earned All-Tournament honors in the 1987 Big East Conference baseball tournament. In 1987 and 1988, he played collegiate summer baseball with the Harwich Mariners of the Cape Cod Baseball League.
He was drafted by the Giants in the 9th round of the 1989 amateur draft. Novoa played his first professional season with the Class A (Short Season) Everett Giants in 1989, and his last season in the California Angels' farm system in 1996.
Novoa never won a game at the major league level but on September 30, 1990, he was able to notch his one and only career save. He pitched the final four innings of a 8–2 Giants win over the arch rival Dodgers. He saved the game for starting pitcher Rick Reuschel. Ironically, this was the 214th and final victory of Reuschel's career.

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