Highlights - England 1-0 Slovenia
Coach Matjaz Kek said Slovenia must look at the positives from their World Cup campaign despite the disappointment of missing a place in the last 16.
Even after a 1-0 loss to England, Slovenia looked set to qualify until a last-gasp winner for the United States against Algeria eliminated Kek's men.
"It's indescribable," said Kek, "Of course we're disappointed but I hope our sport can gain from this defeat.
"I hope in time my players can focus on what they've achieved."
Slovenia went into Group C's final round of fixtures top of the group and knowing a draw would seal their qualification.
But they were outplayed in Port Elizabeth by England, who should have won by a greater margin than the one goal given to them by Jermain Defoe in the 22nd minute, and who have now qualified as runners-up in the group.
Donovan scores late winner for US
Slovenia retained hope that Algeria would deny the US in Pretoria but
As news came through of Landon Donovan's 92nd-minute winner for the US against Algeria in Pretoria, Slovenia's players sank to the turf in despair.
"Our [players] should be left alone for a while as they are feeling very hard moments," said Kek.
The narrow scoreline in Port Elizabeth meant Slovenia remained in the game and, but for some heroic defending from the likes of John Terry and Glen Johnson to deny goalbound shots from Zlatko Dedic and Milivoje Novakovic, they could have snatched the point they needed.
"I congratulate my team and England. I hope England will win the World Cup," said Kek.
"England played well. At the end we could have got a draw but sport is like that, very unpredictable."