It's the first tournament victory for the Manu since Dubai in 2012 and reverses a 42-5 hiding suffered at the hands of their Pacific rivals in pool play a day earlier.
Head coach Damian McGrath was full of praise for his players.
"I never in my wildest dreams when we woke up this morning thought that we could go through the day. We played three probably the most physical teams here in South Africa, Argentina and then Fiji and to put in the sort of performance that we did made me really proud."
Another heavy defeat appeared on the cards for Samoa when tries to Isake Katonibau, Leone Nakarawa and Jerry Tuwai gave Fiji a commanding 21-0 advantage nine minutes into the final.
Belgium Tuatagaloa struck back with a try for Samoa but Jerry Tuwai's second of the match gave Ben Ryan's side a seemingly insurmountable 26-7 half-time lead.
As if to emphasise their strength, Fiji brought on Waisea Nayacalevu and Samisoni Viriviri for the second spell but it was all Samoa as two tries to Tila Mealoi and one for Siaosi Asofolau cut the deficit to two points with two minutes remaining.
And with time up on the clock, it was the captain Falemiga Selesele who completed the fairytale comeback, crossing for the match-winning try.
Damian McGrath admitted he thought his team was dead and buried at half-time but told them to get the first try and take it from there.
"As much as they beat us quite easily last night (in the pool stage) we were again the architects of our own downfall and we spent a lot of time analysing that last night. We didn't lose so much as give it away. Fiji are a good team and we don't need to offer them opportunities and that was our mantra going into the final. We didn't get off the to best of starts but the players stuck to the plan that we hatched and it came good for us. We were coming home with a wet sail in the second half and once we got our foot on the jugular we kept it there and it's testament to the way the players performed."
The Manu had earlier beaten South Africa and Argentina to reach the Cup semis and final for the first time this season.
"I just said that to the boys in the changing room that it's a great feeling but now we will be expected to produce that every time, but if we want to be the team I think we should be then we should be aiming high. I've always felt we were a quarter final team, come what may, and our consistency lets us down. We've proved that over the last two or three tournaments that we can make the quarter finals (and) we've shown today, when our self-belief and resolve is right, we can match it with anybody - and to beat Fiji, after the way they beat us yesterday, is a really satisfying thing."
Damian McGrath said the ultimate goal remained next month's Olympic repechage tournament in Monaco but this was a welcome step along the way.
"It's been a long, hard eight-nine months that players have put in..it's been a long-term plan and that's been hard to do because we've had so much pressure and expectation from home - you know people want instant results - but the players have held their nerve and been patient...I hope we've repaid some of that with this cup win today."
Samoa have risen one place to eight on the overall standings.
Despite missing out on the silverware, Fiji's runners-up finish extended their overall series lead to 14 points with one round remaining.
A quarter final berth in London this weekend will be enough for Ben Ryan's side to defend their crown.