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The Black and Gold (15-4-3) earned its fourth straight victory thanks to goals by Kwadwo Opoku and Carlos Vela.
The Angels lost for the eighth time in their last 11 games as reports circulated that the club is at least listening to trade offers for their two-way superstar.
Thompson's two-run shot in the second inning gave the Dodgers a comfortable lead which they did not squander.
Sitting at 42-57, it's a tall order for the Angels to make the postseason. Trading Ohtani would give the Halos assets for the future.
Under Armour announced two years ago that it was ending its deal with UCLA. The two sides were four years into a 15-year deal worth $280 million, which was the highest in college athletics.
Thursday's quality start may have been Ohtani's last time on the mound at The Big A. The Angels are reportedly listening to trade offers for the reigning AL MVP.
Trea Turner had three hits for Los Angeles, including a three-run double. Pitcher Tyler Anderson improved to 11-1.
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With the loss, the Dodgers' season-high eight-game overall winning streak ended.
The Angels' Noah Syndergaard (5-8) went 5 2/3 innings, allowing one run on six hits and two walks with six strikeouts, but received zero run support.
The native of Ukraine won two championships with the Purple and Gold playing alongside the late great Kobe Bryant and Shaquille O'Neal.
The Halos improved to 3-14 in July after snapping a five-game losing streak on Sunday.
Los Angeles swept a four-game series with the Giants at Chavez Ravine for the first time since 1995 and only the third time in the archrivals' long history.
In his first shot on goal, the former Real Madrid forward netted his first career MLS goal with the Black and Gold.
Trea Turner and Freddie Freeman also homered for the Dodgers, who have won 14 of their last 15 games.