Giovanni Trapattoni admitted he would rather have suffered the heartache of penalty shoot-out defeat that see the Republic of Ireland were dumped out by William Gallas' controversial winner.
The Arsenal defender's extra-time winner came after Thierry Henry appeared to twice handle the ball before crossing, although the offence was not spotted by the officials.
As a result, Ireland lost their play-off 2-1 on aggregate and it is the French and their reprieved manager Raymond Domenech who will head for the finals in South Africa next summer.
Trapattoni said: "I am not only disappointed, I am also sad. It is a bitter evening.
"It's a bitter situation. I would prefer to have gone out on penalties.
"I am sad because the referee had time to ask the linesman. I am sure he should have, and he could have confirmed it was handball.
"I am upset. We speak many times about fair play. I go to schools and speak about fair play. I speak with the young kids about sport. Its important in life.
"Everybody saw the game. You know what happened."
Ireland's dreams were torn apart 13 minutes into extra-time after the ball reached Henry deep inside the penalty area.
He appeared to control twice with his hand before squaring for Gallas, who bundled it home to level on the night and give the French the decisive goal in the tie.
Furious goalkeeper Shay Given led the protests to Swedish referee Martin Hansson and his assistant, but to no avail as France held out to squeeze through to next summer's finals in South Africa.
It was especially hard luck on the Republic, who were the better side for long periods at the Stade de France.
They took the lead on the night when skipper Robbie Keane fired home from Damien Duff's 32nd-minute cross, and had several opportunities to increase their advantage.
John O'Shea fired over from a good position two minutes after the restart and Duff went through one on one with keeper Hugo Lloris with 61 minutes gone, but came away second best.
And so despite not losing any of their six away games during the qualifying campaign, including trips to Italy and France, the Irish slipped to a fifth defeat in six play-off ties as a new heartbreaking chapter in their football history was written.
Assistant boss Liam Brady said it was "a sad day for football", although by then, there was no way back.
Trapattoni said: "France played well in Dublin, but tonight we played better.
"And over two games, we deserved to go to South Africa. But the result is different. We can only wish them well. They can do well in South Africa."
France coach Raymond Domenech's press conference bordered on farce when there was initially no interpreter, although when later questioned about Gallas' goal, he was terse to say the least.
He said: "I did not see a hand. It's you people who are speaking about this.
"Sometimes we feel unlucky like we were against Serbia, sometimes we feel lucky.
"I just want to congratulate the Irish team. I am disappointed for the public and the fans. In a way, I regret that they did not qualify.
"I very happy for the players and the staff and the people here. The only word we need to say tonight is that we are very happy at the qualification."