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The Argentine guaranteed himself one of the top two places in Group B with a 2-1 record, the same as defending champion Federer, who had already sealed a semi-final spot after winning his opening two round-robin matches at the season-ending tournament.
The final day of action in Group B began with seven scenarios, but a three-set win for world number seven Del Potro muddied the waters as the line-up for the semi-finals will now not be known until after the evening match between David Ferrer and Janko Tipsarevic.
Victory for Tipsarevic would see Del Potro top the group, while a win for Ferrer would mean three players are tied on two wins and in that case Federer would top the group because of his superior sets percentage and Del Potro would be runner-up.
Ferrer had been relying on a Federer victory to keep his hopes of a semi-final place alive.
The winner of the group will face Britain's Andy Murray while the runner-up will play world number Novak Djokovic.