The Yankees now have a bona fide closer, but the team’s prospect pool got thinner in the process.

Yankees catching prospects Rafael Flores and Edgleen Perez, along with outfield prospect Brian Sanchez, are heading to the Pirates in exchange for veteran closer David Bednar, The Post’s Jon Heyman reported Thursday.

Flores, 24, was ranked as the Yankees’ eighth-best prospect on MLB Pipeline’s list.

He was terrific in 87 games with Double-A Somerset, hitting .287 with a .842 OPS and 15 homers, and played 10 games with Triple-A Scranton/Wilkes Barre before the trade.

Perez was the Yankees’ 14th-best prospect, according to MLB pipeline, and is just 19 years old.

He hit .209 with 26 RBIs in 83 games for the Yankees’ Single-A affiliate.

Sanchez, not in the MLB Pipeline’s top-30 prospect ranking, is a lefty bat who was hitting .281 in 242 at-bats in Single-A.