One point from a possible twelve against the group's two heavy hitters is a drastic statistic that the Republic's young squad will have to ponder on over the coming months of friendlies and Mickey Mouse matches.
It all went wrong as early as the sixth minutes when an error by Manchester United's John O'Shea and Charlton's Matt Holland was punished by Hakan Yakin, before the Republic's fate was sealed on the hour when Stade Rennais frontman Alexander Frei bundled home the second goal.
O'Shea - playing in the centre of defence in place of the suspended Kenny Cunningham - got himself in a muddle as he failed to clear a straight-forward ball on the edge of the area after only five minutes. Frei drove an angled low cross into the six-yard box and Yakin showed superb composure as he nipped ahead of captain Holland at the far post, skipped round Shay Given and slotted home.
Ireland might have equalised after 10 minutes when Damien Duff – playing on the right with David Connolly partnering Robbie Keane up front - drilled a low ball into the Swiss area. Kevin Kilbane, earning his 50th cap, laid it off nicely for Colin Healy, but the Celtic man snatched at his free shot and screwed it wide. Ireland had another good chance when they won a corner on their left in the 21st minute. Ian Harte curled over an away-swinger and Breen just about had a free header which he planted over the crossbar from eight yards.
Connolly was on the spot after 38 minutes when Duff sent in a deep cross from the right, but the West Ham striker is not the tallest and as he stretched to make the header his effort went wide. Ireland almost conjured up an equaliser four minutes before the interval when Connolly did well to release Duff down the left and his deep low cross was just too far for Keane who sent it into the side netting.
The second half started well for Ireland as Breen's height posed problems for the Swiss defence and there were half-chances involving Duff and Holland. By then, the Swiss had protected their lead by replacing Yakin with Fabio Celestini after 55 minutes, and Kerr sent on Clinton Morrison for Connolly three minutes later. Instead of finding an equaliser, Ireland's fate was sealed on the hour when they conceded their second goal.
Raphael Wicky's cross from the left was met with a downward header by Chapuisat. Given made the save, clawing the ball off his line as he dived to his left, but Frei pounced at the far post to force it into the net.
Goals were now needed, so Kerr's last two substitutions after 74 minutes came as a bit of a surprise as Holland and Healy were replaced by Mark Kinsella and Steve Finnan. Finnan might have been an instant hero as within two minutes he met a cross from Duff with a header which he sent wide.
But Ireland were having no luck in front of goal and Keane in particular had one of his quietest internationals as Ireland made a frustrating exit from the qualifying campaign.
In the other game in Group 10 Russia came from behind to beat Georgia 3-1, earning a play-off spot. Aleksandr Iashvili gave the Georgians a surprise lead after just three minutes in the Lushniky stadium.
But Dmitri Bulykin levelled for the home side after 29 minutes and the Russians went in ahead after Egor Titov struck in first-half injury time.