The Japanese eighth seed was lucky just to be facing the big-serving Croat, having been two sets down in his opener against qualifier Kamil Majchrzak before the Pole suffered muscle cramping and retired mid-way through the fifth.
Against Karlovic, however, Nishikori squandered a two-set lead before closing out a tense tiebreak to prevail 6-3 7-6(6) 5-7 5-7 7-6(7) on a sweltering day at Margaret Court Arena.
Dripping sweat, the former U.S. Open finalist slumped to his knees in relief, having had to save three break points at 4-4 in the fifth set to prevent towering 39-year-old Karlovic from serving for the match.
The first Asian man to ever contest a Grand Slam final, Nishikori joked that Karlovic served as many aces in the match as he would manage in a year.
"Even after a few sets he was serving still really well, and there was, yeah, too many aces and (it was) frustrating, too, you know, for my side," he told reporters.
"I (would) rather do three sets, but today he was playing well, and first match, too, the guy was playing really solid.
"I could (have) lost these two matches. So yeah, I just need to recover well. But, I mean, it's only two matches, so I'm not too tired yet."
The 2014 U.S. Open finalist will nonetheless feel lucky to be alive, having squandered a 6-3 lead in the final tiebreak which has a new first-to-10 points format.
Karlovic was also wasteful, thumping a regulation volley into the net that would have put him within two points of victory.
The 6ft-11in (2.11m) Croat, the oldest man in the second round at Melbourne Park in over 40 years, was unable to serve his way out of trouble and Nishikori nosed in front with a searing return that proved too much for the net-rushing Karlovic's lunging backhand.
Having watched the ball fly past him 59 times from serving machine Karlovic, Nishikori closed out the match with two big first serves of his own, both down the 'T', to set up a clash with unseeded Portuguese Joao Sousa.
A three-times quarter-finalist at Melbourne Park, Nishikori will hope to ride the wave of support from the army of travelling Japanese fans who chanted his name throughout the Karlovic match.
"I feel more support here," he said when asked to compare the four Grand Slams.
"You can tell there are so many Japanese. And also many Asians. I'm sure I feel more comfortable playing this Grand Slam than (any) other Grand Slam."
(Editing by Peter Rutherford/Amlan Chakraborty)
