Muguruza, who will be playing in her first semifinals of this tournament since 2015, needed the win to advance to the semifinals at the expense of Wimbledon finalist Karolina Pliskova. Kontaveit was already assured of a spot in the semis before her last group-stage match.
Muguruza avenged a recent loss to Kontaveit, who beat her in just 48 minutes in the Kremlin Cup quarterfinals in Moscow last month.
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Muguruza's familiarity with the conditions at night paid dividends throughout the match, as the usually laser-sharp accuracy that Kontaveit has used to win 28 of her last 30 matches was conspicuously absent. As Kontaveit struggled to find the measure of the court, Muguruza became the first player to break the Kontaveit serve in Guadalajara, doing so in her opening game.
The WTA Finals are played in a round-robin format with the top two players from each group advancing.
The semifinals will be played on Tuesday and the final is set for Wednesday at the Centro Panamericano de Tenis in Zapopan.