After taking the first set, Djokovic's Japanese opponent saved four break points before levelling.
The match was played there after Novak Djokovic, having played three of his opening four matches away from Centre Court, had his request to play in the main stadium granted.
Having reached the semis of 22 of the 24 majors between 2011 and 2016, Djokovic is now closing in on a first final appearance at a Slam since losing to Stan Wawrinka at the U.S. Open two years ago.
"I thought it was unnecessary to get the warning", Djokovic said as he came off court.
The 12-time major victor prevailed despite picking up two code violations and accusing umpire Carlos Ramos of "double standards".
"I didn't harm the grass, I know how I threw the racket".
That didn't seem to affect his focus, though, and neither did a time violation he was given when serving at 4-2, 30-30 in the fourth set.
"Anything could have happened, so this is a big achievement for me to get to the semi-finals at Wimbledon".
A tight third set turned in Djokovic's favor as Nishikori went wide and that was enough for the fired-up three-time champion to edge back in front as he served into a 2-1 lead.
His troubles began when he copped a code violation for unsportsmanlike conduct for bouncing his racquet into the grass behind the baseline on tennis's most famous centre court early in the third set. And I asked everybody behind me out loud, "What did you hear me say?'".
Nishikori, who had won only two matches in 15 meetings with the 12-time major victor, broke for 1-0 in the fourth but was broken straight back.
"Double standards, my friend".
He then let rip at Ramos for failing to sanction Nishikori for a similar act of frustration in the fourth set.
Djokovic looked to be growing frustrated and was warned for throwing his racket into the ground.
But the 12th seed was not to be denied as he raced into the last four, hitting an impressive 40 winners on the way.
Djokovic created a first break point with an astonishing rally that concluded with a forehand down the line and a fist pump, before capitalizing brilliantly at the second attempt.