It is the first time the 27-year-old Czech has been ranked among the world's elite since a horrific knife attack at her home in December 2016 left her with an injured hand.
"It's a very special feeling to be back", said the world number 21.
Asked how she managed to turn the contest around, Kvitova said: "I have no idea".
However, Muguruza could not convert and Kvitova broke the Spaniard to edge ahead 4-2.
Saving her fourth break point of the set, she narrowly held onto her lead while Muguruza continued to dig for chances with some aggressive play, though she was unable to overhit her opponent.
It was Kvitova's 13th straight win, having come to Doha with victory in St. Petersburg followed by Fed Cup wins. Whereas, Muguruza had a day off after her scheduled opponent, Simona Halep, had to withdraw due to a foot injury which lingered since January.
"When I remember where I was one year ago, it was going to be impossible".
Third seed Muguruza raced into a 5-0 lead in the opening set as Kvitova, who had spent nearly twice as long on court this week as her opponent, endured an error-strewn opening to the match. She then had two more double faults in the fourth game to get broken again, and was trailing 5-0 when she won three games in a row before losing the first set.
A load roar came after the Spaniard sent a forehand wide, and Kvitova ultimately sealed the second set with the same scoreline as the first, displaying a much-better performance as compared to the earlier stages, hitting 16 winners and 16 unforced errors.
The service hold propelled Kvitova to grabbing the first break of the decider immediately, though Muguruza had to unfortunately call for a medical time-out after injuring her knee during a rally. In total, Kvitova faced 11 break points, but only lost her serve in the first set. "I just tried. It was a really tough match, a big fight and hopefully the people enjoyed it". Questioned if it felt more special because of the circumstances of her comeback, she added: "It's something that's wonderful, let's say". Kvitova won with a single break of serve at 6-3.