Defending champions Al Kuwait headed into Tuesday's second-leg encounter at the Stadion Mandala with a slender 3-2 advantage thanks to a dramatic late brace from Ali Al Kandari in last week's first leg.
Having won the competition for the last two seasons in a row, Al Kuwait were considered favourites to make the semi-finals, but found themselves 3-0 down at half-time as Pugliara bagged twice either side of Boas Solossa's strike.
Titus Bonai added a fourth shortly after the break and although Reza Ghoochannejhad scored a consolation for the holders, Pugliara added his third to take home the match ball before Yohanes Pahabol rounded off the rout in injury time after Fahad Hamoud received his marching orders for the visitors.
Persipura made an ideal start as Pugliara broke the deadlock in just the second minute with an acrobatic scissor kick.
The hosts were constantly looking to apply pressure on the counter-attack but a second did not arrive until two minutes before the break when captain Solossa burst through two challenges and his strike from distance beat Al Kuwait goalkeeper Musab Al Kandari.
Incredibly, Pugliara extended the lead in first-half stoppage time and when Bonai finished emphatically at the back post in the 52nd minute Al Kuwait were staring down the barrel of a heavy defeat.
Ghoochannejhad had a goal ruled out for offside shortly after, but the Iran international was not denied a second time when he headed home Fahad Al Enezi's cross with 25 minutes remaining.
Any hopes of an unlikely comeback were quickly extinguished as Pugliara went up the other end and curled home into the bottom right-hand corner for his hat-trick.
Al Kuwait's miserable day worsened when Hamoud was sent off for a second bookable offence in the 68th minute, and the humiliation was complete deep into injury time when substitute Pahabol raced down the right and finished well past Al Kandari.
