Prograis won by judges' scores of 118-109 and 117-110 while the third judge saw Zorrilla winning 114-113.
"I was confident I would get the decision," Prograis said. "It was a tough win but I felt like I deserved the win."
Prograis, who managed the only official knockdown in the third round of a fight filled with pushdowns and slips, improved to 29-1 while elusive Zorrilla fell to 17-2.
"I got the drop early and I kept pressing the action but he ran around the whole time," Prograis said. "I definitely have to go back to the gym and work on some things but he ran, he definitely tried to survive."
Prograis, 34, suffered his only loss in a 2019 title unification showdown with Scotsman Josh Taylor, but the southpaw has won his five fights since then, including an 11th-round knockout of American Jose Zepeda last November for the vacant WBC title at 140 pounds.
Despite his brief tenure, Prograis is the division's longest-reigning champion among major belt holders.
Late in the first round, Zorrilla sent Prograis sprawling with a right but the champion grabbed Zorrilla and pushed him to the ground, prompting referee Ray Corona to declare no knockdowns, instead both being ruled pushes.
"That was a good punch, that right hand he caught me with," Prograis said. "It looks like a knockdown but when I did it, it didn't feel like it. I never was hurt."
Prograis hit Zorrilla in the nose with a hard left hand just under a minute into the third round that sent the challenger to the canvas and midway into the round landed a flurry of punches on the Puerto Rican fighter while trapping him in a corner.
"He was stronger than I thought. He caught me with some punches," Prograis said. "But he just ran around. It was hard to get to him.
"He felt the power when I did drop him and he started running even more."
Fighters traded punches from a distance for most of the middle rounds, each cautiously testing his rival's resolve without taking major risks in a tactical bout.
Prograis went to the canvas on a slip in the 10th round when the left feet of both fighters tangled.
Zorrilla, 29, and Prograis began exchanging inside punches with urgency in the 11th round, sensing the fight remained up for grabs.
Prograis fell forward seconds into the 12th round but Corona ruled a push to the back of his head put him onto the canvas. He rose and they exchanged a few punches to the final bell.
