Baalke will have oversight of free agency, trades and re-signings. He will continue to manage the college scouting and pro personnel departments, roles Baalke held in his previous position as director of player personnel.
Baalke received good reviews after taking charge of the team's draft last month in place of former general manager Scot McCloughan, who parted ways with the 49ers in March.
Team owner Jed York said the 49ers would not have a new general manager in the team's organizational structure. Baalke will take many of GM duties and work closely with York, coach Mike Singletary and vice-president of football operations Paraag Marathe.
The 49ers also named Joel Patten as their new director of college scouting.