Dutch pair Thiemo De Bakker and Matwe Middelkoop rallied from a set down to win 7-6 (7), 4-6, 4-6, 6-4, 6-1 after Federer's regular partner Stan Wawrinka scratched citing fatigue.
Switzerland leads 2-1 with second-ranked Federer due on court at Palexpo arena in the first of Sunday's reverse singles against No. 144 De Bakker.
If Federer loses, Wawrinka is scheduled to play 436th-ranked Jesse Huta Galung in a decisive fifth match.
The hard-court series decides which nation stays in the 16-team World Group next year.
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