McCall's side were undone by an early set-piece and a late counter-attack as their debut in the competition left them needing a momentous comeback in Athens next week to reach the play-offs.
Motherwell had good spells of pressure and possession and a number of half-chances but could not find a way past the visiting goalkeeper.
McCall said: "I think we more than matched them. I don't think the scoreline reflected the performance.
"I just wanted the lads to put in a performance their families and the fans would be proud of and they did that."
Well lasted 13 minutes before an inswinging free-kick from Lazaros Christodoulopoulos evaded everyone and nestled inside Darren Randolph's far post.
The hosts had enjoyed some decent pressure before substitute Charis Mavrias broke away in the 76th minute, after a Motherwell free-kick was cleared, to slot home.
"I'm disappointed with the goals," McCall said.
"We talked about not giving silly free-kicks away with the boy's ability from set-pieces.
"It was a great area to put the ball into and the goalkeeper has to take a step across in case (Jean-Alain) Boumsong gets it.
"We started well and Las (Keith Lasley) had a great chance. The second half we had a real go and created opportunities and with just a little bit of luck...
"But it wasn't to be.
"We always knew their threat on the counter-attack but they played it well. From their point of view it was a good goal."
McCall, who picked a 4-4-2 formation with attacking wide men Jamie Murphy and Chris Humphrey in midfield, added: "We have players who want to score goals.
"We didn't want to go out with a whimper. We were pressing and probing and most people thought the goal was coming.
"It would have been nice if we could have got it to 1-1 but it wasn't to be."
Panathinaikos head coach Jesualdo Ferreira said: "We experienced pressure from Motherwell but whenever we had the opportunity to break quickly we created problems.
"Motherwell work hard and play football that is difficult to control but I thought we deserved the win."
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