The Kenyan veterinarian quickly became the fan favourite but was swiftly broken in the first leg by the Belgian.
Former World Grand Prix champion De Decker would race to the first set but then scraped through the second after Munyua missed multiple darts for the set on double 20.
A miscount by taking 125 out of 135 to leave double 5 at a crucial moment in the match to win the third set almost handed the game to De Decker, but the Kenyan was able to pin it at the first attempt to get on the board and push his opponent into a fourth.
Munyua would then hit six perfect darts before narrowly missing the seventh as he attempted to break, before miscalculating again and hitting double 16 instead of tops - as well as getting attacked by the wasp - allowing De Decker to steal.
A spirited effort from the qualifier in the fourth would see him at one point leading De Decker 2-1 in legs, but a 130 checkout would level things up at 2-2, with darts in hand for the world number 18.
Three missed match darts opened the door for Munyua, however, and he took out 38 to capitalise and force the deciding set.
Seven perfect arrows would open the fifth set for De Decker, who duly took the first leg with an 11-darter to break.
A bullseye finish on 135 levelled the set with an immediate break back, the first ton-plus of the match at a pivotal moment for Munyua, before a polished double 10 would put him ahead in the tie and one leg away from a stunning victory.
Tops would then seal the deal in one of the greatest upsets ever seen on the Alexandra Palace stage.
'It is humbling'
"It is amazing," Munyua told Sky Sports after the mammoth victory.
"I didn't expect it. But now it has happened, and I'm happy about it.
"It is a very big moment for the sport itself, for Africa and Kenya. It is humbling. The sport can grow. I'm happy I did my best.
"I'm happy the miscount didn't affect me. I came back and still got the momentum, was focused and concentrated. I'm just happy the game didn't go foul.
"Thank you so much. Why not?"
Munyua averaged 80.78 to De Decker's 83.83 but was superior on the doubles, registering 33.33 per cent (12/36) to the Belgian's 24.44 per cent (11/45).
The 30-year-old will face the winner of Kevin Doets and Matthew Dennant.
Super Sakai arrives
Earlier in the session, Motomu Sakai announced himself in emphatic fashion at the worlds, producing a standout performance to sweep past Thibault Tricole and ignite Alexandra Palace on his tournament debut.
The Japanese qualifier overcame a lively start from Frenchman Tricole to claim a 3-0 victory, combining sharp timing on the finishes with a clear appetite for the stage.
A nerveless 121 checkout proved pivotal in the opening set, swinging momentum decisively and setting the tone for what became a surprisingly one-sided contest.
Tricole, making his third appearance at Ally Pally, struggled to convert opportunities at crucial moments.
Missed doubles repeatedly opened the door, and Sakai - whose on-stage antics were lapped up by the Ally Pally crowd - was quick to step through it.
The Tokyo thrower punished errors with increasing confidence, notably landing a 148 finish in the second set to tighten his grip on the match. From there, the balance rarely shifted.
By the third set, Sakai looked fully at ease, feeding off the crowd and maintaining control even as both players wobbled on the outer ring.
A 14-dart break of throw effectively sealed the result, before Sakai closed out victory on double 5 to a rapturous response from the stands.
Sakai averaged 87.38 throughout the contest, with both players sinking two maximums apiece. He'll face Sweden's Andreas Harrysson in the second round.
Joyce and Rydz through
Elsewhere in the afternoon, Ryan Joyce advanced with a straight-sets win over Owen Bates, capitalising on superior doubling to move into round two, while earlier Callan Rydz navigated a patchy display to see off debutant Patrik Kovacs 3-0 in the day's first match.
The action continues at Ally Pally later on Thursday evening, with former champion Michael van Gerwen taking to the stage alongside other big names including Dave Chisnall and Fallon Sherrock.