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.
Federer, Wawrinka to clash in all-Swiss Australian Open semi-final
The top half of the draw has already lost world number one Andy Murray and offers rather smoother sailing than a bottom half, which features multiple grand slam winners Novak Djokovic, Rafa 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.
Grand Slam win on Nishikori’s mind
"I was serving well," the 31-year-old said. "I think I'm moving better and better, and it's all positive so far. I'm feeling good in my body, so that's the most important."
Nishioka, who gave Nadal a run for his money in Acapulco at the start of the month, surprised even himself with his victory over Berdych.
"I tried to do my best, but today I couldn't figure out how could I beat Berdych," Nishioka said. "I tried to find a way, and then I think he give me a little bit of a chance. My body was feeling like I cannot move that much, but I just stayed focused and tried to fight. And then I found a way."
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