The Czech is in the semi-finals for the second straight year after falling last season to eventual champion Victoria Azarenka.
Trailing 5-2 in the second set, Spain's seventh-seeded Muguruza battled back, saving two match points as they went to a second tiebreaker.
It was to no avail, however, as Pliskova notched her sixth win in seven meetings with Muguruza.
"Definitely the best match for me in this tournament," Pliskova said. "It was a good player, so the level ultimately goes a little bit more up.
"Definitely from the baseline I think was fine. But the way I was finishing those sets, I'm not happy with that," added Pliskova, who admitted that failing to convert match points when she had them preyed on her a bit in the second-set tiebreaker.
"I had some good rallies on my hand and on my racquet, but didn't serve well in important moments. So everything was through the rally, which is always tough for me," said Pliskova, who leads the WTA Tour in aces and relies heavily on her big serve. "So I'm happy that I stayed there and closed it in the second tiebreak."
The Czech, who is the highest-ranked player in the draw thanks to the injury withdrawal of Serena Williams and the fourth-round exit of Angelique Kerber, is in the semi-finals for the second straight year after falling last season to eventual champion Victoria Azarenka.
She's aiming to add a third title of 2017 to those she has already won in Brisbane and Doha.
In the semis she'll face eighth-seeded Russian Svetlana Kuznetsova, who defeated compatriot Anastasia Pavlyuchenkova 6-1, 6-4.
Kuznetsova needed just 63 minutes to power past her 19th-seeded countrywoman, who had come out on top in the pair's two meetings in the past three months.
Kuznetsova, 31, is a two-time Grand Slam champion who last year returned to the top 10 for the first time since 2010.
She reached back-to-back Indian Wells finals in 2007 and 2008, but has never lifted the trophy.
The remaining women's semi-finalists will be decided on Thursday, when seven-time Grand Slam champion Venus Williams takes on Russian Elena Vesnina and 2011 Indian Wells champion Caroline Wozniacki faces France's Kristina Mladenovic.
Williams, who ended a 15-year boycott of the event last year but lost in the second round, is after a first Indian Wells title.
The 36-year-old American, who saved three match points in her opening victory over former world number one Jelena Jankovic, says she's enjoying tennis more than ever.
"I feel like I'm the most joyful now, honestly," said Williams, who made a scintillating run to the Australian Open final where she fell to her sister Serena.
"I've clearly loved the game. You have to, to play this long, to deal with the pressure and to put in the amount of work that it takes," she said. "But I definitely feel like I'm peaking in terms of the love level."