The world number one wasted three match points before suffering a 6-4 6-7 (8-10) 7-6 (7-2) defeat to the Argentinian on Sunday.
Federer served for a sixth Indian Wells title at 5-4 in the third set but Del Potro fought back before Federer played a poor tie-break.
The Swiss said the defeat would hurt, but he took plenty of positives from the tournament as his record slipped to 17-1 this year.
“I feel frustrated, you know, that I let an opportunity like this go by. Serving 40-15, any game I probably win – I don’t know what the stat is – 90-something per cent,” he said, via the ATP World Tour.
“So it should sting, like you said, for a bit. The question is how long? It won’t be long, but it’s disappointing talking about a great match like this, losing, even though I was right there.
“Obviously there is not too much time to dwell over it. Like I said, I’m happy for Juan Martin.
“It’s a tough one. And I still had a good week here. I still see the positives at the end of the day.”
“It’s a bit disappointing but that’s how it goes,” Federer says in press. “But well done to him. I lost my serve a little bit (in the tiebreak) and he was clean.”