Kyrgios won that match, eventually going on to compete against Rafael Nadal in the final.
Hours later Kyrgios, whose undoubted talent has often been betrayed by his quickfire temper, made a statement on Twitter apologising.
"My shoulder started to hurt in the practice today which didn't help either and once I lost the first set I was just not strong enough to continue because I've not eaten much the past 24 hours".
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The Australian, who has also pulled out of his scheduled doubles encounter alongside partner Lucas Pouille on Wednesday, took to social media to offer a reason for his action.
Only previous year, he was fined $21,200 and hit with an eight-week suspension for tanking against Mischa Zverev in the second round of the same tournament. Kyrgios was consequently suspended.
But Schwartzman cut the 185cm Federer down to size and an unusually error-strewn performance from Federer was summed up when he squandered an easy backhand volley at the net to go to the first-set tie break, which the Swiss eventually won 7/4. However, he did not undertake a medical examination after leaving the court.
Kyrgios and Johnson were both comfortable on their serves and they went into the tie break with signs Kyrgios was beginning to lose his cool.
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"What's happening here?" he was overheard saying, seemingly irritated by spectators moving around between.
"What is he doing?"
Meanwhile, Kyrgios has been confirmed to play at the Brisbane International.
And when he was hit with a point penalty, Kyrgios said: "Poor officiating again".
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Johnson wrapped up the set and Kyrgios shook the hands of his opponent and the umpire - though not looking him in the eye - and left. Last year Kyrgios was suspended and fined more than USD50,000 for a freakish outburst which saw him throw a 6-3 6-1 match against German Mischa Sverev while asking an umpire, "Can you call time so I can finish this match and go home?"