SNL later won the Emmy for Outstanding Variety Sketch Series and Shookus went up onstage to join her colleagues as creator Lorne Michaels gave his acceptance speech.
Shookus and Affleck sat with the SNL stars in the auditorium and when the show was announced as the winner, the actor stood up to let them walk to the stage. He laughed when Michaels spoke and smiled as he watched the cast victoriously walk offstage.
He then got up by himself during the commercial break and walked back into the VIP area, chewing gum. Shookus joined him and was seen holding onto his arm as they smiled and looked at each other. They also chatted with and hugged Dave Chappelle, who won an Emmy for his guest spot on SNL at the preliminary Creative Arts Emmys earlier this month. The comedian wore sunglasses as they talked.
Affleck and Shookus then exited the VIP area with their arms linked.
Alec Baldwin later won the Emmy for Outstanding Supporting Actor in a Comedy Series for portraying President Donald Trump on SNL and thanked Shookus and other cast and crew of SNL in his acceptance speech.
Affleck and Shookus were later spotted in the winners' walk area, with her holding her Emmy statuette. The two chatted with another unidentified female Emmy winner about where to go after the Emmys.
"All I want to eat is pizza," Shookus said.
Affleck then took a photo of the two women.
SNL was nominated for 14 Emmys this year.
Shookus last won an Emmy in 2015; she shared the award for Outstanding Variety Special for the Saturday Night Live: 40th Anniversary Special.
E! News had learned in July that Affleck is dating Shookus. They are both notoriously private about their personal lives and have not commented about their relationship but have been spotted out together many times, mostly in Los Angeles and New York.
Affleck last attended an Emmys ceremony in 2005, when he arrived with then-wife Jennifer Garner. The actor has been nominated for four Emmys in the past, for Project Greenlight.