Lindpere found former Crew midfielder Dilly Duka at the far post for a right-footed stab that tied the game 1-1 in the 52nd minute.
Two minutes later, Lindpere assisted on Magee's 10th goal, sending a cross into the box that Magee chested into the goal.
Magee has scored in four league matches and six straight in all competitions since being acquired from Los Angeles in May.
The Fire (5-7-3) are 3-0-2 in their past five matches and have won six of the past seven against the Crew.
Federico Higuain scored on a penalty kick in the seventh minute for Columbus (5-6-5).