Aiyuk had been listed as questionable for the game.
The 49ers announced Thursday they elevated receiver Chris Conley from the practice squad for the game.
Aiyuk suffered the injury on his first catch in Sunday's game against the Los Angeles Rams, a 30-23 49ers victory. He finished the game with three catches for 43 yards.
Aiyuk leads the 49ers this season with 172 receiving yards and two touchdown catches in two games. He has 11 receptions, tied with Deebo Samuel for the team lead.
He was named the NFC Offensive Player of the Week after Week 1, when he had eight receptions for 129 yards and two touchdowns in the 49ers' 30-7 victory over the Pittsburgh Steelers.