The undefeated 23 year-old cruised through every round without much fuss until the fight was stopped in the final round of eight to save Flores from further punishment.
Morales is taking tentative steps towards a world title shot over the next twelve months, which could either come at super-flyweight or his current weight of 118lbs.
The win represented a 16th knockout for Morales – who is a chip off the old block and looks a certainty to win a recognised title belt in the near future.
Also on the bill at the Forum in Inglewood, Kazakh prospect Ruslan Madiev made it five straight wins in the pro ranks by knocking out Julio Sanchez in the second round of their contest. The 22 year-old had his opponent in trouble in the first and finished him off just 20 seconds into the next session to score a third KO.
Earlier, female flyweight Seniesa Estrada dropped Carly Batey on her way to a six-round points win. Judges carded 58-55 twice and 57-56 as Estrada moved to 4-0, whilst Pedro Duran stopped Daniel Perales in the final round of six and is now 11-0.