Despite the loss, Nadal will move back to No. 1 in the ATP rankings next week for the first time since 2014, before a series of injuries affected his game.
Simona Halep moved a step closer to the world No 1 ranking after easing into the quarter-finals of the Western & Southern Open with victory over Anastasija Sevastova.
The sixth-ranked Spaniard reached her first U.S. event final by flipping the script in a rematch of their 2016 Cincinnati semi-final.
The results (third round): Men: Grigor Dimitrov bt Juan Martin del Potro 6-3, 7-5; Yuichi Sugita bt Karen Khachanov 6-7 (0), 6-3, 6-3; David Ferrer bt Pablo Carreno Busta 6-4, 6-4; Jared Donaldson bt Nikoloz Basilashvili 6-4, 7-6 (4); Dominic Thiem bt Adrian Mannarino 7-6 (4), 7-6 (3); John Isner bt Frances Tiafoe 7-6 (4), 7-5.
Halep has yet to drop a set in the tournament and appears to be peaking at just the right time, looking to become the first Romanian women to claim the top ranking.
"I think she played very solid, not missing much and obviously serving well".
"I'm not playing my best tennis, but winning when I'm not playing good is a plus for me", Halep said.
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Pliskova, last year´s US Open runner-up, had won six matches in a row over Muguruza since losing their first meeting at the 2013 French Open.
Muguruza will play for her fifth career title Sunday against the victor of a later match between Romania´s second-ranked Simona Halep and 151st-ranked U.S. wildcard Sloane Stephens.
"Whatever comes I will just take it", said Pliskova. I just feel good. "Everything went my way".
Both face the prospect of a long day Friday - an early afternoon match and, if they win, another at night. Pliskova, who played part of one match and all of another on Friday after rain forced postponements on Thursday, had 28 unforced errors to Muguruza's 13. That followed a 2-hour, 18-minute win over Madison Keys on Thursday, when she fought off three match points. "It's not going to help me". Obviously tough schedule for me last two days: three matches in about not even 24 hours.
Kyrgios, ranked 23rd, took the first set in 25 minutes, dropping only three points on his serve while taking seven- of eight points off the 31-year-old Spaniard's second serves.
Nonetheless, Muguruza broke serve in the first game of the match to set the tone for the afternoon and never looked back to roll to victory in one hour, 19 minutes, capping the match by winning a marathon break on her fifth match point.
She gained a second-set edge with a backhand victor on break point for a 4-2 lead before closing it out.