Nishikori, 22, outlasted Tsonga over three and a half hours to win 2-6 6-2 6-1 3-6 6-3 and advance to his maiden grand slam quarter-final.
"I am feeling unbelievable, to beat Tsonga makes me really happy," he said.
"I was playing one point at a time, it was not easy conditions and he was playing well too. Hopefully it's big in Japan, I'm really excited."
Tsonga admitted: "It was tough, I had a good opponent today. I didn't play good tennis and I didn't control everything. It was not a nice moment for me.
"He's tough to play because he runs a lot and everything comes back."
Nishikori will meet Andy Murray next. The fourth seed took just 49 minutes to advance after Mikhail Kukushkin was forced to retire through injury after losing the opening two sets.
David Ferrer eased through to the quarters with an easier-than-expected victory over Richard Gasquet.
The fifth-seeded Spaniard, a semi-finalist here last year, won 6-4 6-4 6-1 and will now meet Novak Djokovic, who overcame a scare to beat Lleyton Hewitt 6-1 6-3 4-6 6-3.
Australian Open Day 8 Men's 4th Round Results
Kei Nishikori def. Jo-Wilfried Tsonga 2-6 6-2 6-1 3-6 6-3
David Ferrer def. Richard Gasquet 6-4 6-4 6-1