Alexander Zverev defeated the usually unflappable Swiss 6-3, 6-7 (7/9), 6-3 in a dramatic match that saw Federer twice hit the ball out of the court in anger and row with the umpire.
A decision on the game in Yokohama will be made on Sunday when officials are able to assess the level of damage from Typhoon Hagibis, which has already forced the cancellation of two games due to be played on Saturday.
Wales' 27-19 win over Fiji on Wednesday had guaranteed the Wallabies a place in the last eight, with the Welsh playing minnows Uruguay on Sunday in a match that should see them book the pool winners' spot.
The Nike Oregon Project was set up to end the distance-running dominance of the east Africans but has become a huge headache for the US sportswear giant, which said Friday it was shutting it down.
Prop Luan de Bruin returns from injury replacing Erich de Jager. Louis Fouche will be starting on centre due to Dries Swanepoel being sidelined by a calf injury.
The star batsman was just two runs away from batting great Don Bradman's Test tally of 6,996 runs and needs four more for his seventh double hundred in the five-day format.