Jamal Musiala and Bright Arrey-Mbi, both 17, started at the Wanda Metropolitano on Tuesday, with Bayern having already clinched top spot in Group A, while fellow teenagers Angelo Stiller and Joshua Zirkzee came off the bench.
Martinez said Champions League holders Bayern had plenty to look forward to, hailing their young talent.
"They were born in 2003 – that's almost when I started to play in the first division," he said, via UEFA.com.
"But Bayern is a club that builds from the bottom with the youth players. The future is bright. When young players train with us, they play very well.
"They are the future of the club."
Bayern failed to land a shot on target in the first half of a Champions League group game for the first time since October 2009.
But Muller's 47th Champions League goal – 21 more than any other German in the competition's history – earned them a draw.
"I am very pleased with this result," Bayern head coach Hansi Flick told a news conference.
"I think we did very well in the second half, we tried to turn the game around – and in the end we got a 1-1 draw. I think we did better after Thomas Muller came on and also Serge Gnabry.
"Also, I am happy for the young players, for some of them it was their first match and then in a such a nice stadium against Atletico. It was a good evening for us.
"We also got some insights that we will discuss with the coaching staff, we will analyze this game and take something with it for the future. But overall I am very pleased."