Top seed Djokovic defeated unseeded Jeremy Chardy of France 6-4 6-4 in the earlier semi-final.
A three-time champion on the Canadian hardcourts, Djokovic has a 19-8 career record against Murray and has won their last eight meetings since the Scot beat Djokovic in the 2013 Wimbledon final. Murray has claimed two Canadian titles.
Djokovic, who received treatment on a sore right elbow several times during changeovers, showed no signs of distress on the court as he dismissed Chardy in a tidy one hour, 20 minutes to run his record to 10-0 against the Frenchman.
"I didn't allow Jeremy to find his forehand too much; one break per set was enough to win the match, could have done some things better but a win is a win," said Djokovic, who did not face a break point the entire match.
"It the (elbow trouble) comes and goes, now is not very pleasant.
"Every day is a new day, I try to bury the pain, play with the pain, it is part of what we do."
He said it was par for the course for every athlete in professional sport to have "something troubling" him.
Chardy, who needed three hours and three tiebreaks to get past John Isner in the quarter-finals, got the match off to a shaky start when he handed Djokovic a break, with the help of a couple of double faults, to open the match.
That was all Djokovic would need with Chardy unable to apply kind of any pressure.
Djokovic got the only break of the second set in the fifth game and then held serve as Chardy again left the court without taking a set from the Serb.
It was a welcome low-stress match for the Serbian, who was pushed the brink of elimination in his Friday quarter-final, during which he survived two match points to beat 87th-ranked Latvian Ernests Gulbis.
In the late semi-final, Nishikori appeared to be fatigued in the second set as Murray won 12 of the final 13 points.
"I think I'm more tired," the Japanese fourth seed said.
"Everything was sore these couple of days. Today it got a little bit worst so I couldn't really move 100 per cent.
"Especially after the first set, I was feeling it more and more. At the beginning of the first set I was okay, but after that I wasn't the same player."
(Reporting by Steve Keating in Toronto; Editing by Andrew Both/Greg Stutchbury)
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