Wawrinka is building up to the French Open which he won in 2015 but his career has been badly affected by a recent knee injury that required surgery and meant he had only won three matches all year before Wednesday.
The Swiss star, twice a champion in Geneva, only got on to court just after 9pm due to rain at the Swiss venue.
He will face Hungary's world number 60 Marton Fucsovics in Thursday's quarter-finals.