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The second-seeded Wawrinka stopped after a medical timeout more than 2 hours into his match with Feliciano Lopez, who was leading 6-4, 2-6, 4-3.
The 10th-ranked Wawrinka has won only five matches — all against players outside the Top 50 — in seven visits since reaching the 2005 final of his home tournament.
The fifth-seeded Lopez will face Robin Haase of the Netherlands in the clay-court tournament on Saturday. The 57th-ranked Haase beat 2011 champion Marcel Granollers of Spain 5-7, 6-3, 7-6 (5).
Daniel Brands, who beat Federer, failed to build on that success in losing 6-3, 6-4 to Victor Hanescu. The 2008 Gstaad champion, Hanescu forced one service break in each set.
The sixth-seeded Russian saved three match points in the tiebreaker.