Djokovic, an 11-time Grand Slam champion whose three titles this year include the Australian Open, downed Belgian 15th seed David Goffin 7-6 (7/5), 6-4.
The 28-year-old Serbian will try to match the career record of six Miami crowns won by Andre Agassi by capturing his third consecutive title at the hardcourt event.
"It's a privilege just to be mentioned alongside Andre Agassi," Djokovic said.
Sixth seed Nishikori, the 2014 US Open runner-up, downed Australian 24th seed Nick Kyrgios 6-3, 7-5.
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Djokovic has a 6-2 career edge over Nishikori, including five wins in a row, most recently in this year's Australian Open quarter-finals.
"It's going to be tough for sure. He has been playing well," Nishikori said. "I played him in Australia. I will try to come up with something better."
Djokovic won his 15th consecutive Miami match and the 29th of his past 30, but only after winning a tense tie-breaker and taking the lone break of the second set, prompting a post-match kissing of the court.
"I wanted to make sure the court feels my love," Djokovic said. "A little kiss for goodbye and I'll see you in two days. I've had so many beautiful memories on that court. It's one of my favorite courts."
He could claim the Miami-Indian Wells double for the third year in a row and his 63rd career title on Sunday.
Squared 4-4 in the tie-breaker, Goffin hit an overhead smash that Djokovic sent back as a lob inside the far baseline to keep the point alive and later took full advantage by winning it with a forehand drop volley winner.
"I was a bit fortunate in the tie-breaker but I made him play the extra shot," said Djokovic.
Goffin, who will jump to a career-best 13th in next
week's rankings, hit a forehand wide to give Djokovic two set points, then saved one on a drop volley winner but lost the set when the ball deflected off the edge of his racquet as he leaped to reach another Djokovic lob.
"Against Djokovic you have to go for the shot in every point," Goffin said. "If you're not there for a few seconds you lose the game."
Djokovic has reached the final in 19 of his past 21 events and in 11 consecutive ATP Masters Series events. He could win a record 28th ATP Masters crown, surpassing the mark he now shares with Rafael Nadal.
Nishikori broke Kyrgios for a 2-1 edge and held from there, claiming the first set after 29 minutes when the Aussie double faulted away a break.
"My serve just let me down," Kyrgios said. "I felt rushed out there. I was looking for answers. He was too good."
"At the net I was very confident," Nishikori said. "I thought I played a good point."
Nishikori, who won his fourth consecutive Memphis title in February, reached his second ATP Masters final, the other coming in 2014 at Madrid.
"He is somebody that has been around and played so many matches on the big stage," Djokovic said. "I don't see him being too overwhelmed or nervous."