The reigning European champions headed into the second leg of their UEFA Champions League semi-final with Real just one goal behind from the first meeting in Spain.
They ended Tuesday night five goals adrift on aggregate, with Real sweeping to a convincing 4-0 victory at the Allianz Arena to book a final appearance in Lisbon.
Bayern never got going on home soil, as they fell two behind inside the opening 20 minutes, with set-pieces and an inability to contain Real on the counter costing them dear.
Guardiola, who conquered Europe on two occasions during his time in charge of Barcelona, said afterwards: "If you don't play well and you defend set-pieces badly, that's just how it is.
"We are playing at the highest level in Europe, and such mistakes are punished right away. Bayern are a big side. I will try to lift the players again."
Club captain Philipp Lahm echoed the thoughts of his boss, with Bayern getting their game management wrong.
He said: "The disappointment is huge. We did not play well tactically, we played an open game way too early.
"While we controlled the first leg, we gave them an end-to-end game today, that's not our way of playing, they like it though."
Playmaker Arjen Robben was kept quiet by a disciplined Real defensive unit and he has called on Bayern to pinpoint what went wrong, but then lift themselves for the challenges which lie ahead.
The Dutchman said: "We had lots of hope, the mood was good. We attacked from the first minute, then conceded two from set-pieces, not counter-attacks.
"We've been punished and have to accept it. A 4-0 defeat at home is tough but we have to lift our heads, we have a cup final soon.
"We received a 4-0 beating today. Accept it. Cry about it. Go home. Then move on."
Bayern legend Franz Beckenbauer, now honorary president, is also looking for Guardiola's men to accept defeat gracefully and write their midweek showing off as an uncharacteristic blip.
He said: "There are those days where nothing works out for you and everything the opponent does works out for them. This was one of those days.
"Congratulations to Real Madrid, they played very well today and absolutely deserve their place in the final."