The Spaniard was stronger in the decisive moments as he pulled through for a 6-3 3-6 7-6(5) 7-6(3) victory, celebrating with an outpouring of emotion rarely seen from him in the first week of a Grand Slam.
The fiery Kyrgios threw everything he had at Nadal - including an extraordinary 143mph second-serve ace - and undoubtedly had him rattled before the Spaniard eventually prevailed.
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It was the best match of Wimbledon's opening week as, amongst the expected histrionics, both men hit the heights with some relentlessly powerful and accurate serving in particular.
Nadal started strongly, got pegged back as Kyrgios fuelled himself with fury in a second set full of incident, then came through a high-octane tiebreak to take the third.
The 43rd ranked Kyrgios then gave a reminder that amid all the antics there is a player of huge quality, one of the few with the weapons to challenge the game's dominant trio, with 33-year-old Nadal the one he seems most able to unsettle.
Nadal was in complete control in the early stages and Kyrgios seemingly needed an injection of emotion – or anger – to fire him up. The Spaniard duly provided it with his slow-motion movement between points and a surprise toilet break after the first set. “Why am I waiting to serve?” Kyrgios asked the umpire – the first of a series of progressively angry exchanges.
The Australian made his mark when he blasted a 143mph (230kph) second serve-ace - the fastest serve of any sort during the tournament so far and the second-fastest second serve in ATP history. He followed up with another ace – via a gentle under-arm lob – though still lost the first set comfortably.
Kyrgios was far more impressive in the second, breaking early with a fierce forehand down the line that saw the crowd erupt as they realised they were in for a real match. That was underlined when Nadal broke back to love – only to drop serve a second time as Kyrgios levelled the match.
If it made the Australian happy, however, it was hard to tell as he kept up a running dialogue with the umpire, which earned him a warning. “You're no-one. You think you're important. You have no idea what's going on. You're a disgrace,” he said.
When Kyrgios did concentrate on his tennis, he was full of invention and variety - introducing an Ali shuffle after his big winners and upsetting a rival he already had history with by launching a return straight at him at the net, earning a glare in return.
Nadal, with 18 Grand Slam titles to his name, was somehow playing second fiddle on Wimbledon’s Centre Court to a mid-ranked player who tells anyone who will listen that he barely cares whether he wins or loses.
Five years ago, of course, he stunned the Spaniard here in the win that announced him to the world and the 24-year-old came into Thursday’s game with a 3-3 career head-to-head record.
Adding spice to the showdown was the Australian's recent interview where he described Nadal as "super salty" and gracious only in victory.
Nadal did his best to rise above it all, though he also exploded with emotion after a huge service hold during a stupendous third-set showdown which the Spaniard eventually took on a tiebreak.
The fourth set was less theatrical, yet just as gladiatorial, as both men found extra power and consistency in their serving to go to 6-6.
Perhaps, typically, however, the tiebreak was effectively settled when Kyrgios netted the most straightforward of overheads on the opening point and Nadal never looked back.
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