Eighth seed Wawrinka captured an early break to surge 3-1 clear and saved three break points before serving out the set, the first time he has captured a set off Nadal in 13 matches.
With both players serving strongly in a smouldering start, the match suddenly came alight in the fourth game when Nadal made his first double-fault and Wawrinka crunched a passing shot to bring up two break points.
In a tense rally, the Swiss ratcheted up the pressure, with a big crosscourt forehand that Nadal was only able to parry into the net.
Without a hint of nerves, Wawinka blasted two aces before holding to lead 4-1, leaving the Rod Laver Arena crowd stunned.
The nuggety 28-year-old then tested the Spaniard again, punching a commanding backhand volley to raise another break point, but the Spaniard saved it.
Serving for the set at 5-3, Wawrinka stumbled, unable to land a first serve for five consecutive points, to concede three break points.
He saved them all as Nadal's returning went awry and he took the set with a cross-court ace.