Spanish coach Luis Aragones was unhappy over the free kick awarded to France which led to the second goal in the 1998 World Cup winners' 3-1 victory.
Referee Roberto Rosetti blew for a foul when Thierry Henry went down after a tackle by Spain defender Carles Puyol.
Aragones said: "Their second goal came from a free kick that wasn't a foul and we were punished by a refereeing error.
"When players give everything you can't ask any more. They're still young and have another chance in the future."
Aragones added: "Football is unjust sometimes, but not always. France were very tough opponents."
Goalkeeper Iker Casillas was unable to contain his frustration at Spain's exit.
"We were so close. It was undeserved, an undeserved defeat," said Casillas.
"But that's football, we're heading home and there's nothing we can do about it."