As the on-court temperature hovered around 40 degrees, world No.60 Hewitt applied the blowtorch to the Japanese young gun in a huge shot in the arm ahead of the Australian Open.
The former world No.1 plays the winner of Federer's semi-final with eighth-seeded Frenchman Jeremy Chardy at Pat Rafter Arena later on Saturday.
Either way, two-time grand slam champion Hewitt is still enjoying the best start to a summer since 2005 when he made the Australian Open final against Marat Safin.
Both Hewitt and Nishikori spent breaks between points with ice packs draped around their necks and on the back of their heads while nestled next to court-side fans as they tried to counter the sweltering conditions.
And at first world No.17 Nishikori defied the draining weather.
Hewitt, 32, was up 40-0 serving at 5-all but was still broken before Nishikori sealed the first set with a stunning backhand winner.
Rather than drop his head and succumb to the heat, Hewitt again showed his fighting spirit to break Nishikori - eight years his junior - in the 10th game and seal the second set.
On a roll, Hewitt rattled off a total of five straight games to jump to a 3-0 lead in the third and didn't look back.
Hewitt moved to a 2-0 overall record against Nishikori, who he last defeated at Wimbledon in 2011.
Fit again after a career-threatening toe injury and back in the world top 75 for the first time in three years, Hewitt is suddenly feeling very good ahead of the year's first grand slam.
"I love the battle," Hewitt said of his fightback on Saturday.
"Mentally this is a major win to have come back and gone the distance.
"You do all the hard work in the off season so you don't want to come here and go through the motions.
"You are retired a long time. I want to squeeze out everything I possibly can before then."