The Swiss third seed romped past Philipp Kohlschreiber 7-5 6-3 and will next face Nishioki rather than Berdych after the 21-year-old Japanese overcame a 6-1 5-2 deficit for a stunning 1-6 7-6(5) 6-4 win over the 13th seeded Czech.
The top half of the draw has already lost world No 1 Andy Murray and offers rather smoother sailing than a bottom half, which features multiple grand slam winners Novak Djokovic, Rafael Nadal and Roger Federer.
Wawrinka needed just 78 minutes to improve to his career record against Germany's Kohlschreiber to 5-0, whipping a trademark backhand winner down the line to end the third round contest at Indian Wells.
"I was serving well," the 31-year-old said. "I think I'm moving better and better, and it's all positive so far.