Carolina Panthers' Luke Kuechley replaced Willis on the All-Pro First Team while Second-Team honors went to the Cincinnati Bengals' Vontaze Burfict and the Arizona Cardinals' Karlos Dansby.
Among the 49ers' team-issued awards, wide receiver Anquan Boldin won the Bill Walsh Award that coaches appoint to the team MVP. Boldin is in his first season with the club.
San Francisco coaches also recognized right guard Alex Boone with the offensive linemen's Bobb McKittrick Award and Smith with the Matt Hazeltine Iron Man Award, both for their courage and inspiration.
Rookie safety Eric Reid received the Thomas Herrion Memorial Award from coaches for making the most of his opportunity as a first-year starter.
Running back Frank Gore, defensive lineman Glenn Dorsey, and special teams ace Bubba Ventrone were honored by players and coaches as the Blue Collar Players of the Year.