The 19-time Grand Slam winner made 36 unforced errors before beating Japan's Nishioka 7-6 (7/4), 6-4 in two hours and seven minutes.
Unbeaten Spain — who won the revamped Davis Cup in Madrid in November — finished top of Group B with world number 10 Roberto Bautista Agut downing Go Soeda 6-2, 6-4 to secure the tie.
Nadal has yet to drop a set but he looked sluggish at times ahead of the Australian Open, where he aims to equal Roger Federer's record tally of 20 Grand Slam titles.
The long exchanges against an unwavering Nishioka seemed to take a physical toll on Nadal, who appeared weary in Spain's first day-session tie in the hot Perth conditions.
"It's the first time I played under these heavy conditions, so the feeling on court is completely different," Nadal said. "I played against an opponent who has started the season on fire."
Nadal struggled to find his rhythm against the defensive prowess of 24-year-old Nishioka, who counter-attacked superbly to break twice in an engrossing first set, but couldn't close it out in the 10th game.
Nadal capitalised and drew first blood after claiming a tense tie break.
The 33-year-old remained under pressure in the second set and was forced to fend off three break points in the sixth game, before eventually pulling away.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ