By Gabriel Tan at the Choa Chu Kang Stadium
Heading into the game 2-1 down from Wednesday's first leg, the Protectors fell behind after 14 minutes when Shimpei Sakurada headed home a corner, although they immediately hit back when Frederic Mendy equalised with a clever lob a minute later.
Franklin Anzite then headed home a cross from Qiu Li to hand Home the lead at the break, but that was cancelled out seven minutes into the second half when Mislav Karoglan tapped home from close range after good work from Tatsuro Inui down the right.
Mendy looked to have forced extra-time when he grabbed his second of the game in the 71st minute, but eight minutes from time, Inui curled home a sublime freekick to send the Warriors through to the semi-finals of the competition.
Despite having one of the best attacks in the Great Eastern-YEO's S.League, Home coach Lee Lim-saeng has admitted several times this season that it is at the back where his side are most vulnerable.
12 minutes into Monday's clash, that nearly cost them again when a long ball from Daniel Bennett was allowed to bounce all the way through to Fazrul Nawaz, although the Singapore international failed to hit the target with his half-volley with only Nazri Sabri to beat.
However, it took the Warriors only a couple more minutes to find the breakthrough, when Sakurada leapt high to meet an Inui corner and glanced his header into the far corner.
Nonetheless, the visitors pulled level a minute later when Mendy latched onto a long pass by Anzite, and caught Shahril Jantan out with a ingenious lob that the veteran keeper failed to keep out despite getting a hand to it.
Buoyed by their equaliser, Home started to push forward with more regularity and were unfortunate not to go ahead in the 38th minute when captain Shi Jiayi fired in a freekick that forced Shahril into a terrific save at full stretch, before the Warriors custodian did well again a minute later to keep out a low shot by Qiu at his near post.
But there was little he could do two minutes before the break when Qiu swung in a cross from the left straight onto the head of Anzite, who expertly planted his header into the back of the net.
The visitors then threatened to undo all their good work four minutes into the second half when Nazri inexplicably spilled a straightforward catch from a headed back-pass from Rosman Sulaiman, but in an even more curious turn of events, Fazrul somehow failed to put the ball into the unguarded net.
Three minutes later, his striker partner Karoglan showed him how it was done when he positioned himself perfectly inside the six-yard box, and was left with a simple tap-in to make it 2-2 after Inui had glided past Rosman down the right and cut the ball back across the face of goal.
Six minutes later, SAFFC should have gone ahead when Shukor Zailan picked up the ball on the right side of the box and drilled in a shot that was parried by Nazri straight at Aliff Shafaein, but from eight yards out, the former Tanjong Pagar winger could only send his follow-up effort wide.
And that miss came back to haunt the hosts in the 71st minute when Mendy grabbed Home's third, after he picked up the ball just inside the area and held off the challenge of Bennett, before smashing the ball into the roof of the net from an extremely tight angle.
Three minutes later, Aliff missed another glorious opportunity to score when he sent a close-range header straight at Nazri, after a delicate chip from the edge of the area by Inui had come back off the crossbar.
Still, the Warriors continued to press and they duly made it 3-3 eight minutes from time when Inui, who netted a terrific freekick to open the scoring last Wednesday, repeated his heroics. This time, he opted for a low, curling effort but again, he expertly found the corner with his strike and left Nazri rooted to the spot.
There was still one final chance for the Protectors to grab a fourth and force the game into extra-time when substitute John Wilkinson latched onto a loose ball on the edge of the area, but he sent a ferocious half-volley just over, leaving SAFFC with a semi-final clash against Gombak United to look forward to.
SAFFC: Shahril Jantan, Razaleigh Khalik (Noh Rahman 81'), Daniel Bennett, Marin Vidosevic, Zulfadli Zainal Abidin, Tatsuro Inui, Shukor Zailan, Shimpei Sakurada, Aliff Shafaein (Ruzaini Zainal 85'), Fazrul Nawaz, Mislav Karoglan (Erwan Gunawan 90').
Home United: Nazri Sabri, Nor Azli Yusoff, Sofiyan Abdul Hamid, Kenji Arai, Rosman Sulaiman (Firdaus Idros 53'), Franklin Anzite, Song Ui-yong, Shi Jiayi, Qiu Li, Indra Sahdan Daud (John Wilkinson 69'), Frederic Mendy.