Baer enrolled at Michigan in 1951. In May 1952, the "Associated Press" wrote that Baer "sparkled" in spring practice, leading Michigan head coach Bennie Oosterbaan to say, "He's going to be a real football player. I don't know if he'll be ready by fall but he could be." As a sophomore in 1952, Baer started three games at fullback, but was used principally as a backup for Dick Balzhiser and Bob Hurley during the 1952 and 1953 seasons. He started six games at fullback for the 1954 Wolverines. Baer's best game for the Wolverines came in a 34-0 win over Minnesota on October 23, 1954, as he gained 94 rushing yards on 17 carries (5.5 yards per carry) and scored two touchdowns. The following week against Indiana, he rushed for 92 yards on 22 carries (4.2 yards per carry) and scored one touchdown. In his final game for Michigan, he gained 75 yards and averaged 6.3 yards per carry against Ohio State. Baer played for the Wolverines on defense as well as offense and was considered "a vicious tacker and a hard runner." After the 1954 season, Baer was selected as the Most Valuable Player on the 1954 Michigan football team. He was also selected to play in the Blue-Gray All-Star Football Classic. He scored the winning touchdown for the blue team on a fourth-quarter touchdown pass from Missouri's Vic Eaton.