Kvitova broke Muguruza's serve five times in a row to seal the first set and take a commanding lead in the second.
It was the first meeting between the pair since Kvitova beat Muguruza in the 2018 final of the same tournament. They played Saturday in front of a sparse, socially distanced crowd.
Kvitova moves to a 28-10 record in career finals and has won two of her three finals in Qatar after losing to Aryna Sabalenka last year.
"It's been great the whole week," Kvitova said. "I just feel like home a little bit. I love the court."
Kvitova's previous tour title was in Stuttgart in April 2019.
The Czech player's run to the title came after a slow start to 2021 including a second-round exit at the hands of Sorana Cirstea at the Australian Open.