Tokyo - The Injury-hit South African Sevens side narrowly lost the Tokyo Plate Final 14-10 against Fiji on Sunday morning.
Earlier, they lost their Cup quarter-final against England and got the better of Wales in their Plate semi-finals. The Blitzbokke remain in third place in the HSBC Sevens World Series standings on 105 points.
Australia became the fifth Cup winner of the season, Matt Lucas slotting a brilliant conversion from out wide in the last minute to help his side beat Samoa 28-26 in dramatic fashion.
South Africa lost two key forwards on Saturday when Boom Prinsloo and Frankie Horne were both ruled out of action with concussion. They also lost promising utility back William Small-Smith with a shoulder injury early in the first half against Fiji.
Despite the injury setbacks, South Africa refused to give up and only desperate tackling by Fiji prevented the Blitzbokke from scoring the decisive third try.
Fiji led 7-5 at half-time after Branco du Preez replied with an unconverted try to the opening score of Waisea Nayacalevu. Nikola Matawalu scored after the break to stretch the Fijian lead, before Chris Dry scored South Africa's second try after a period of sustained pressure.
The South Africans launched several attacks towards the end and each time their runners were stopped just in front of the tryline by the strong Fijian defence.
Earlier in the day, England got the better of South Africa by winning a close encounter 21-17, which meant South Africa had to contest the Plate division.
The Blitzbokke then won the semi-final 22-10 against Wales to set up another crunching encounter against Fiji. South Africa's coach Paul Treu said his team performed admirably despite the two huge setbacks on Saturday.
"We lost Cecil Afrika and Paul Delport before the tournament and the loss of Frankie and Boom depleted us further. When William Small-Smith came off against Fiji we were down to just nine players.
"Our guys gave it their best despite all the setbacks and I can't praise them enough for their effort. They refused to give up, and with a bit of better fortune against Fiji, we might have won that game. We will now go back to the drawing board and make sure we are ready for the last two tournaments in Glasgow and London," said Treu.
South Africa will play Wales, Scotland and Russia in Pool D of the Glasgow Sevens on 5 and 6 May.