Pablo Armero had put Colombia ahead after only five minutes with a deflected goal.
"You can't make excuses when you lose 3-0," Santos told reporters after the game. "We had good spells of play and all we can do now is look at the next matches.
"The score doesn't show it, but I think we played well. But these games are turned on the details, and they didn't work for us today. We're still proud to be here, and we'll continue to play hard.
"We should have done better in the finishing, I don't think we were worth a 3-0 defeat. But unfortunately that's football. There are three games, we only lost one. It's a big success to be here, but we have to win too."
Greece are currently bottom of Group C, but Japan and Ivory Coast are yet to play their opening match.