Tottenham scored the first goal of the Champions League encounter through Son Heung-min, but then saw Bayern score four unanswered goals to take a commanding lead.
Though Harry Kane's penalty in the 61st minute made it 4-2, the Bundesliga side were rampant as the game reached its conclusion, scoring three times in the game's final 10 minutes to condemn Spurs to a humiliating defeat.
Serge Gnabry would end the game with four goals while Robert Lewandowski scored a pair in a clinical performance for the away side.
After the game, Pochettino insisted he was happy with some aspects of his side's display and demanded that Spurs remain mentally strong after a tough result to swallow.
"I think we played 30 minutes really well," Pochettino told BT Sport . "We started the game really compact, intensive, pressing high. We were unlucky that we conceded at the end of the first half in the last section for 2-1.
"Of course, afterwards they were very clinical. You will see there was not very much difference in shots or attempts, but they were very clinical. And after eight or nine minutes of the second half it was 4-1.
"After we scored the penalty for 4-2 we had some chances to score the third and be in the game, but from 83 to 88 [minutes] we conceded three more goals.
"Tough, tough result. It's too much and too hard to accept this kind of result, but this is what happens when you have the quality like today, [Bayern were] very clinical in front of goal.
"We are very disappointed, very upset, but we need to stay all together and show a message of togetherness and stay strong in our mentality."
After Tottenham went all the way to the Champions League final last season, they appear to be very far away from making a similar run in this season's competition.
Pochettino explained that even though his side's appearance in Madrid came just a few months ago, it was already irrelevant in terms of this season's results.
"Football is about today, not yesterday. Football is always about the … motivation, I do not know the word you use, but it is always about the show," Pochettino said.
"You need to work to show today and tomorrow, because it is not about experience, not about what happened three months ago. Football is about playing today and giving your best and today we're disappointed and Bayern were very clinical.
"It's a difficult situation. It's tough to have that difficult situation against you. You need to be strong and keep going, to stay all together and help each other.
"That's the best medicine. Not to find who is guilty or escape the situation. When you receive this type of result, it's important to bounce back and believe in yourself."