Howard Wilkinson’s side lost 3-1 and lose vital ground in group nine and now lie in third place behind Greece and Germany. England fell three goals behind inside an hour and only a late Michael Carrick strike narrowed the deficit.
It was the loss of control in the final minutes that will concern Wilkinson as much as the defeat; Luke was red-carded for an injury-time push on Giorgos Theodoridis and then Under-21 skipper Terry took the long walk for a crunching challenge on Giorgos Kyriazis.
"Whatever the circumstances the players have got to learn to stay in control," said Wilkinson. "They have been taught enough about it. It's vital you learn to keep in control. At this level they are told their behaviour level has got to be even more respectable than normal.
"Luke felt, whether it was accidental or not, that he had got a smack in the face and responded with a shove. John said he had got the ball and this was supported by other players but I pointed out that at this level more often than not that tackle is deemed to be reckless.
"They have got to learn. It is as simple as that."
Wilkinson, however, had no gripes over the end result which England facing an tough assignment if they are to qualify for next year's finals.
"We were beaten by a better team but I felt it was another one of those results England have in the summer after young players have played a lot of football.
"That is not good for performance in terms of continuity but we can still qualify although we may now have to get a result in Germany before we finish with two home games."
The Greeks took the lead after 26 minutes, Giorgis Kyriazis burst past Matthew Upson and Sean Davis before clipping a ball across goal to Dimitris Papadopoulos who made no mistake with a glancing header.
The second arrived on 42 minutes when the ball broke to Giorgos Vakouftsis after Luke had challenged Sokratis Petrou and he drilled his shot past the exposed Bywater. A Terry own-goal added to England’s woes, his backward header creeping under the body of goalkeeper Stephen Bywater.
Luke Young was dismissed towards the end of England’s European under-21 Championship qualifying defeat to Greece in Athens on Tuesday evening.