Wawrinka was trailing No. 5 seed Feliciano Lopez of Spain 6-2, 2-6, 4-3 when he threw in the towel and send Lopez on to the semifinals.
Sixth-seeded Mikhail Youzhny of Russia advanced with a 5-7, 6-4, 7-6 (9-7) win over fourth-seeded Juan Monaco of Argentina. Youzhny saved three match points to reach Swiss Open semis for the second time in three years.
Youzhny will face Victor Hanescu, who topped Daniel Brands of Germany 6-3, 6-4.