Both players were forced off during the first half of the 1-0 defeat in Germany, with Siqueira hobbling from the field in the 38th minute with a muscular problem before then being promptly followed down the tunnel by Saul, who took a heavy blow to his chest.
"Siqueira suffered a hamstring strain on his left thigh," read an Atletico statement. "For his part, Saul Niguez suffered a kidney trauma with a hematoma.
"He underwent tests, ultrasounds and CT scan. He has been admitted to the Leverkusen Clinic for observation."
Atletico can ill afford to have either man unavailable for the second leg on March 17, with both Tiago Mendes and Diego Godin having been ruled out of the game at the Vicente Calderon through suspension.
Before then, Diego Simeone's side face Sevilla, Valencia and Espanyol in La Liga, as they fight desperately to hold on to third place in the standings.