A source confirmed the split to E! News. Affleck, 46, and Shookus, 38, dated for about a year and split two to three weeks ago.
"They are still very amicable and have stayed friends," a source told E! News. "They both tried to make it work, but the distance just proved to be too much for them right now. Family comes first for them both."
On Thursday, the day after Affleck celebrated his 46th birthday, the Justice League actor was seen at the Japanese restaurant Nobu in Malibu with Shauna Sexton, a 22-year-old model who was Playboy's Miss May 2018.
"They weren't affectionate but seemed to have a fun dinner," a source told PEOPLE of the dinner. "He ordered for them and took care of the check. They chatted across from each other. She looked very cute, and he seemed interested."
The source said the dinner gave off a vibe that it "looked like maybe a first date."
After news of the dinner broke, Shookus took down her Instagram account.
Affleck and Shookus were last seen together on July 23, when they were visiting Puerto Rico together while Affleck was on a break from filming.
Sources previously told E! News that Shookus chose not to move to Los Angeles as they had planned. On Valentine's Day, the couple went house hunting in the Pacific Palisades area and things were still serious between the two in June. Affleck even went on a double date with Shookus' parents in Santa Monica.
"He feels it is over with Lindsay," an insider said.
Affleck was previously married to Jennifer Garner from 2005 to 2015. The couple's divorce has not been finalized though, and a judge reportedly threatened to end the proceedings if they cannot come to an agreement soon. However, Garner is reportedly in no rush because she wants to see Affleck "work on his health and sobriety" first.
"Ben would have liked to have finished this and closed the books sooner," a source recently told Us Weekly. "Jen just isn't willing to settle the custody issues until she's 100 percent certain that he's clean. She'll wait for him to prove he is taking it very seriously."
Affleck and Garner have three children, Violet, 12; Seraphina, 9; and, Samuel, 6.
Shookus was previously married to producer Kevin Miller, with whom she shares a 5-year-old daughter. Shookus also won an Emmy last year for Saturday Night Live and has another Emmy for the SNL: 40th Anniversary Special.
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