Rodriguez earned a free kick in the 67th which Bale took and Atletico goalkeeper Miguel Angel Moya punched out straight to Kroos, who miskicked and skied the ball.
Kroos then stabbed the ball weakly in the 75th minute, giving Moya an easy catch, and Benzema headed over the bar three minutes later.
Raul Jimenez substituted Mandzukic in the 78th for Atletico and Di Maria came on for Modric to reinforce Madrid's midfield.
Two minutes after Rodriguez's goal Casillas saved a shot by Koke and before Garcia equalized for Atletico.
The Bernabeu erupted with protests from its fans as Atletico midfielder Mario Suarez appeared to handle the ball in injury time, but the referee did not award the sought-after penalty.
The second leg is to be played Friday at Atletico's Vicente Calderon Stadium.
Despite having scored an away goal, Atletico coach Diego Simeone said his team's chances of winning the cup were still only 50 percent.
"We are going to find ourselves up against a team with many attacking options and very good players," he said of the second leg.