The Scot, 29, won 6-1 6-4 and will play Spain’s Rafael Nadal or Juan Martin del Potro of Argentina in the gold-medal match on Sunday.
Murray, assured of at least a silver medal, hopes to become the first player to win two Olympic singles titles.
He won his second Wimbledon and third Grand Slam title last month.
“It’s obviously not an easy thing to do, that’s why it’s never been done before,” Murray said about the prospect of another gold medal.
“I’m going to give my best effort and I’m happy I’m guaranteed the medal, but the goal is obviously the gold medal and give it my best effort to win another one”.
After coming through two gruelling matches to reach the last four in Rio, Murray dominated against Nishikori, breaking serve for a second time to win the first set in 30 minutes.
The Briton was unhappy to receive a code violation in the second set as he argued with umpire Carlos Ramos, but he remained in control of the action on court.
Nishikori appeared to visibly wilt in the Rio heat as he dropped serve midway through the second set with a dreadful game.
Murray served his way to an unexpectedly straightforward victory, winning arguably the point of the tournament, a 23-shot rally, to set up a third match point.