Garner says she became "hyper-protective" after the news of her pregnancy "got out when I was in the middle of my first trimester."
"I hadn't even had a chance to tell my friends. That alone was so ugly," she says in an interview in the September issue of InStyle, now on newsstands.
Garner and Affleck were wed June 29. "We were able to have a beautiful, private wedding, and I couldn't be happier," the 33-year-old actress says.
"If we were just chatting I would tell you everything, but I feel uncomfortable with people reading too much about my pregnancy or my relationship," she tells the magazine. "It grosses me out. It's too sweet to read about or dissect or talk about."
Garner stars as Sydney Bristow on the ABC spy drama "Alias," which returns Sept. 29 for its fifth season in a new Thursday night time slot.
ABC has announced that Garner's character will also be expecting a baby.