By Gabriel Tan at the Jalan Besar Stadium
Erwan Gunawan was the hero for the Warriors, coming off the bench to net deep into added-time after Warriors midfielder Shimpei Sakurada struck 12 minutes from time to cancel out a Shahril Jantan own-goal in the 25th minute.
The victory was a fitting send-off for SAFFC coach Richard Bok, who had confirmed earlier in the season he would be leaving at the end of the campaign after seven years in charge, and regardless of what happens in their final Great Eastern-YEO's S.League game next week, 2012 will now be viewed as a success.
Their opponents Tampines entered the game looking to complete part one of a potential double, with their title fate in the league to be decided next Friday with both them and second-placed DPMM FC in action against Harimau Muda and Balestier Khalsa respectively.
SAFFC, on the other hand, were looking to win their seventh major trophy under Bok, and they certainly warmed up for the final in style with a 6-1 league win over Gombak United on Monday.
The star of the show that night had been Tatsuro Inui, who laid on three assists with his brilliant deliveries, and he carved out the first chance of the night in the 11th minute when he burst down the left and whipped in a good cross that Mislav Karoglan met at the near post and just fired wide.
Watch: Highlights: SAFFC win Singapore Cup... More Videos
Karoglan was looking ominous early on with his movement and touches and he took up another good position inside the area two minutes later after Sakurada had won the ball from Jufri Taha and forced his way down the right. Thankfully for the Stags, Benoit Croissant was alert to the danger and weighed in with a vital interception before the Japanese midfielder's pass could reach the SAFFC spearhead.
The Warriors were certainly starting the brighter of the two teams and they were unlucky not to take the lead in the 18th minute when a delightful freekick by Inui came smashing back off the crossbar having beaten Sasa Dreven all ends up.
However, it was Tampines who finally broke the deadlock against the run of play seven minutes later, although plenty of the blame will be laid on Shahril, who inexplicably pushed a harmless left-wing cross by Ismadi into his own net, leaving his team-mates looking on in bewilderment.
Six minutes after the half-hour mark, the Warriors came close to an equaliser when another dangerous cross from Inui nicked off a defender and bounced right at the feet of Dreven, who did just enough to push away the ball from the danger zone.
In what was turning out to be a very open encounter, it was the Stags' turn to carve out an opening in the 41st minute when a visionary pass from Mustafic Fahrudin sent Jamil Ali racing down the right. Unfortunately for them, the 28-year-old opted to shoot instead of squaring the ball to the unmarked Sead Hadzibulic, and ended up sending his effort straight at Shahril.
Jamil was presented with another opening right on the hour mark when a lovely reserve ball by Hadzibulic sent him racing down the left, but before he fire a shot away, Marin Vidosevic put in a strong challenge to slam the door shut in his face.
Eight minutes later, it was Hadzibulic's turn to threaten the SAFFC goal when he escaped the attentions of both Daniel Bennett and Vidosevic and immaculately brought down a visionary pass by Croissant down on his chest, only to send his half-volley over the bar.
With time fast running out, the Warriors began to push more men forward in search of an equaliser and 15 minutes from time, Dreven did well to fist away a searching diagonal ball from Bennett, especially with Karoglan waiting to pounce at the far post.
Nonetheless, there was nothing he could do three minutes later when Inui swung in a corner that was flicked on at the near post by Bennett, straight to Sakurada who reacted brilliantly to stab the ball into the back of the net.
Inui, who was causing real problems to the opposition defence every time he received the ball, called Dreven into action again in the 85th minute with a searching cross that was headed for Karoglan, and two minutes later, the Croatian goalkeeper had to deal with a shot from the edge of the area by the Japanese, who had made his way into the middle after a mazy run from the wing.
With the clock ticking down fast, the game looked set for extra-time but with one final push forward, Zufadli Zainal Abidin charged down the left and whipped the ball into the box, where it eventually made its way to Gunawan.
The 25-year-old took one touch to bring the cross under control before laying it right to Karoglan, who skipped inside his marker before unselfishly laying it back to his team-mate. From 15 yards out, the SAFFC substitute made no mistake with an emphatic finish that sailed into the roof of the net despite a strong hand from Dreven, handing his side the Singapore Cup in the most-thrilling of fashions.
SAFFC: Shahril Jantan, Noh Rahman, Daniel Bennett, Marin Vidosevic, Zufadli Zainal Abidin, Aliff Shafaein (Erwan Gunawan 71'), Shukor Zailan (Ruzaini Zainal 63'), Shimpei Sakurada, Tatsuro Inui, Fazrul Nawaz, Mislav Karoglan.
Tampines Rovers: Sasa Dreven, Benoit Croissant, Mustafic Fahrudin, Jufri Taha, Imran Sahib (Ahmed Fahmie 80'), Sazali Salleh, Ahmad Latiff, Ismadi Mukhtar, Jamil Ali, Sead Hadzibulic, Aleksandar Duric.