The fifth game of the third set was nearly a mirror of the third game of the second - which Nishikori had held despite three break points.
Three-time champion Djokovic, seeded 12, will face Japan's 24th seed Kei Nishikori for a place in the semi-finals.
"I thought it was unnecessary to get the warning", he told the BBC after the 6-3 3-6 6-2 6-2 win.
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Djokovic rallied to hold and only lost two more games from that point onward as he advanced to his first Grand Slam semi-final since the 2016 US Open. But he grew frustrated after failing to capitalize on three straight break points in the third game of the second set and was given a code violation after slamming his racket into the ground. "I guess there are other factors that play in".
"I like the level of tennis that I'm playing on right now", Djokovic said. I think that these performances here at Wimbledon have been the best I've had in the last 12 months.
The loss marks the end of world No. 28 Nishikori's most successful ever Wimbledon appearance, having reached the final eight for the first time in his career. (Ramos) said he didn't see it.
"It motivates me to do extremely well here because I don't want to sit here and explain my loss". But then the Japanese player, world number four in March previous year, survived those four break points early in the second set to level.
Djokovic, seeded 12th, was visibly disappointed at those missed opportunities, incurring a warning from umpire Ramos for throwing his racket, and Nishikori made him feel even worse when he broke to lead 3-1 after Djokovic put an attempted drop shot into the net. "I hope I can get a chance to fight for a trophy".
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This time it was the Serb who saved three break points before he let out a huge roar when, with momentum on his side, he broke Nishikori in the next game.
"After that he was playing better".
Asked whether he was a "man on a mission" to get back to where he left off, the Serb could only agree: "Of course, that's why I'm here", he said.
'I didn't harm the grass.
Djokovic won a dozen major titles before a loss of form, and injury problems, affected his game following his first French Open triumph in 2016.
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