Willis was the only San Francisco player named to the NFC team, although four 49ers were chosen as alternates, including tight end Vernon Davis.
Willis, the second-year pro who leads the 49ers with 153 tackles, was mildly surprised to learn of his second trip to Hawaii.
"I really didn't think I was going to make it back over there this year," Willis said, citing the 49ers' 5-9 record late in their sixth consecutive losing season. "Just looking at the situation, I was just like, 'No, there's no way I'm going to be able to make it back."'
Willis, who returned his only interception this season 86 yards for a touchdown, also cited the 49ers' improved offense for limiting his chances to make the Pro Bowl. He was the NFL's defensive rookie of the year in 2007, but his numbers are slightly down this season.
"Any real person could see that if you're out there on the field a lot, then you're going to have the opportunity to make more plays," Willis said. "This year, it was a lot different. Our offense was out there, they were running the ball, they were taking time off of the clock, and they were putting up points. ... I'll take that over being out there 80 and 90 snaps a game, any day."
Punter Andy Lee, a Pro Bowler last season, is an alternate this season along with Davis, the mercurial tight end who has emerged as one of the league's best blockers. Kick returner Allen Rossum and special teams standout Michael Robinson also were chosen as alternates.