With a shot at the International Boxing Federation (IBF) flyweight title of Masamichi Yabuki on the line, Fajardo needed just 65 seconds to get the job done.
Just four seconds into the fight, Fajardo landed a wicked left hook that sent Reyes crashing to the floor.
A second knockdown followed and Reyes wisely waited until the third man on the ring counted to eight before getting up.
But at the 40-second mark, Fajardo scored the third knockdown with Reyes still visibly shaken from the early onslaught.
On panic mode, Reyes pulled off a trick by spitting out his mouthpiece so he could buy more time to recover.
But even after almost 15 seconds of added time, Reyes was still shell-shocked and a flurry that was highlighted by another left hook sent Reyes down and the referee immediately called a halt to the contest without issuing a count.
Fajardo, who arrived in Argentina three days before the fight after enduring a 38-hour trip from Manila, ran wild across the ring as the crowd, looking forward to a celebration at the Club Atletico Santa Paula, was left in shock.