Kyrgios then ran up to his opponent, shook his hand and walked off court to boos from the crowd, leaving Johnson and chair umpire Fergus Murphy confused.
Local media reported that Kyrgios received two code violations during the set and was docked a point in the tiebreak.
Reports also said he told officials he would quit if he lost the set, but Kyrgios took to Twitter to apologise to his fans.
"I've been battling a stomach bug for the past 24 hours and I tried to be ready but I was really struggling on the court today which I think was pretty evident from the first point," Kyrgios said.
"My shoulder started to hurt in the practice 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 in the past 24 hours," he added.
"I'm hoping to be okay for the doubles and will make a decision tomorrow morning, hopefully off of a good night's sleep which I didn't get last night.
"I'm gutted to be honest to be honest as I was keen to keep the good momentum that I built in Beijing going and finish the year strong. I'll do what I can to make sure I do."
Kyrgios was fined $16,500 by the ATP last year for deliberately throwing a game away during his second-round defeat by Mischa Zverev in Shanghai.
Argentine Juan Martin del Potro overpowered Russian teenager Andrey Rublev 6-3 6-4 in the second round.
American Sam Querrey powered past Yuichi Sugita 6-3 6-2 and Canadian teenager Denis Shapovalov beat Viktor Troicki 6-7(3) 6-3 6-0 in first-round matches.
(Reporting by Shrivathsa Sridhar in Bengaluru, editing by Ed Osmond)
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