Estrada dominated most of the fight, outboxing Srisaket and winning the majority of the rounds on the judges' scorecards at the Forum arena in Los Angeles.
The 32-year-old Srisaket looked slow and flatfooted early on compared to the confident Estrada who welcomed the toe-to-toe exchanges in the centre of the ring.
There were no knockdowns but Estrada landed a powerful overhand right in the eighth that rocked Srisaket's head back. He won by scores of 116-112, and 115-113 twice.
Srisaket, who fights mainly as a southpaw, looked strongest in the final two rounds when he seemed to be re-energized after switching from an orthodox to a lefty stance.
Estrada appeared to slow near the end of the 12-round fight when he got caught with some solid punches by the Thai champ. But the Mexican survived and won the fight based on his superior performance throughout the first 10 rounds.
A former WBA and WBO champion in the flyweight division, Estrada improved to 39-3 with 26 knockouts. Coming into Friday's bout Estrada had won twice since losing to Srisaket in their first fight in February of last year.
The loss snapped Srisaket's 20-fight win streak as he dropped to 47-5 with one draw and 41 knockouts. This was the fourth defence of the title he won in a stunning upset over Nicaragua's Roman 'Chocolatito' Gonzalez in 2017 in his US debut in New York.
It was Srisaket's first loss in five years.
On the undercard, Danny Roman unified the WBA and IBF super bantamweight titles by defeating TJ Doheny by a majority decision. Roman won by scores of 116-110, 116-110 and 113-113.
Roman, 27-2 with one draw and 10 knockouts, has won 19 fights in a row since dropping a 2013 decision to American Juan Reyes.
Mexico's unbeaten Rey Vargas, the 33-0 WBC champion, is believed to be next on Roman's radar.