"It upset me because I didn't understand why we had to be in your book, because we really didn't have anything to do with this," Jada told her guest, sharing she was "hurt" by the mention.
Remini admitted to not thinking of how sharing a story would reflect on the power couple.
"Looking back on it, I didn't even consider Jada and Will," she said.
"I was so caught up in that pain," she added, getting choked up, "and also the pain of others and the effects that it had."
The night in question came up in July 2017 when "WWHL" host Andy Cohen brought up an evening when the Smith family spent time with famed Scientologist Tom Cruise.
"(Cohen) doesn't tell you what he's going to talk about. He just throws stuff at you, and so when that came up, I was like that's not how I remember that night going," Smith explained. "You had basically created a situation for Will and I... At that point, I'm like, I got to protect Will and I."
"When I saw it, I was hurt, because I was like, 'Oh, she's in (the church)," Remini responded.
"When I saw that you made that statement, I felt the need to respond to something that I felt was untrue and was an attack," Smith said.
She denied being a Scientologist after Remini's Daily Beast interview on Twitter writing: "I practice human kindness, and I believe that we each have the right to determine what we are and what we are not... NO ONE ELSE can hold that power."
"My grandmother was like, 'You're gonna learn all the religions, and then you got to decide which one you want to practice,' " Smith told Remini around the table. "So, for me, all religions have been my home, which is why I didn't have a problem going to the Church of Scientology and saying 'I'm not a Scientologist. I want to just be here and see what you have to offer,' because that was my life, that's what I'm used to."
She added: "I always took the position that I'm here at the Scientology Center to learn what I want to learn, and I have no interest in being a Scientologist."
Toward the end of their chat, Remini offered Smith her heartfelt apology: "I really truly deeply apologize. I should have thought about the names in the book, I should've thought about what that meant for you guys, and I didn't.'
"It's OK. I love you anyway," Pinkett Smith said, to which Remini echoed: "And, I love you anyway."
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