"The lads were absolutely magnificent from start to finish," Flynn told BBC Radio Wales Sportstime programme. "Wales will be proud of them, I'm sure of that, as I am tonight."
The Welsh lads now face a play off, the draw for which is made this Friday in Malmo, Sweden.
The 14 teams in the play offs are:
Group winners:
Italy
England
Switzerland
Austria
Germany
Turkey
Spain
Finland
Serbia
Wales
Runners up:
Belarus
France
Israel
Denmark
None of the runners up will play each other. The two legged play off will take place the same time the senior teams faces Lichtenstein and Germany in the 2010 World Cup Qualifiers.
The seven winners of the play off games will join hosts Sweden for the U21 European Championships in Sweden in 2009.