After knocking down Marquez late in the opening round, Filipino-American Viloria saw his early-round dominance end in the fifth as his opponent launched a strong second-wind onslaught.
But Viloria weathered the blows before scoring a second knockdown with the third coming after a minute of round 10 and proving decisive as the corner’s towel came into the ring.
Viloria, who won the title from Julio Cesar Miranda in July of last year, paid tribute to the bout-winning left to Marquez's head afterward.
"I think my left hook was too fast for him," said Viloria, whose record now stands at 32-3 after his 19th career knockout in his sixth straight victory.
Mexico fighter Marquez’s career tally now reads 34-3 with 25 career knockouts.
In other world title action underneath the main event, Nicaraguan Roman Gonzalez took a unanimous points decision over Juan Francisco Estrada to retain his WBA light flyweight strap.
The undefeated Gonzalez moved his professional career to 34-0 with scores of 116-112, 116-112 and 118-110 though he was unable to add to his 28 stoppages against the rugged Mexican, now 21-2.
Gonzalez may now view a step up in weight to take on Viloria as the next career step.