Nishikori fought back from one set down to record a 6-7 [1-7] 6-4 6-4 victory over the number four seed in China.
After the match, Frenchman Tsonga conceded that there was really little he could have altered to defeat Nishikori.
"He's really talented, especially when everything works," Tsonga said. "Today he didn't miss one drop shot. He played really well. He returned unbelievable. I think nobody breaks me many times like this."