In what was Wilder's first defence of the title he won in January, the 29-year-old sent Molina to the canvas on four occasions, but three times the Texan returned to his feet.
However, there would be no continuing after a right-hand in the ninth round had Molina reeling before follow ups took him down to floor for a final, decisive time, with referee Jack Reiss stopping the fight at 1:03 in the ninth round.
Wilder maintained his unbeaten record, and is now 34-0, with 33 of those coming courtesy of a knockout. However, Saturday's victory didn't come easily.
The Alabama native was forced to weather some early blows from Molina who looked to make good on his pre-fight assertion that he would hurt the champion.
Molina landed a strong right in the third round and followed it up with further blows Wilder's head, but the former Olympian remained standing.
Wilder than began to gain the upper hand, and sent Molina to the canvas in fourth and twice in the fifth. Molina withstood a further barrage in the sixth, and bounced back in the eighth round, finding the body of Wilder with a number of punches.
Molina could not get back to his feet on the fourth occasion though, and referee Reiss called time on the fight, with the heavy favourite victorious, but with Molina having lasted a lot longer than many predicted.