Flannigan is one of four changes made to the starting line-up which pipped Ireland 14-13 a fortnight ago.
Blues Academy Flanker Adam Powell joins Rhys Shellard in the Back Row and there are also starting positions for Blues players Duane Goodfield, Tom Riley, Rhys Gill and recent hat-trick hero Chris Czekaj.
There is also a first appearance in the Wales U21 squad for Bath centre Tom Cheeseman, who makes the bench.
Backs coach Dai Rees is also in Australia with the Wales Sevens squad and his place is filled by Wales national skills coach Neil Jenkins.
The former Wales and Lions fly-half, who scored a world record 1,049 Test points, has been shadowing Rees but now steps up a level to join Simon King as an assistant coach.
Wales U21 head coach Chris Davey said: "Simon is in his second season with us, helping with the forwards, and Neil has been helping with his goal-kicking expertise.
"But, with Dai away in Australia, Neil is now expanding his role with the backs and it is great to have him in the environment - he is a legend and the boys love having him around."
Wales Under-19s take on Italy in their Six Nations match at Aberavon RFC on Thursday night (1900 GMT).
Wales Under-21s: Aled Thomas (Dragons Academy); Aled Brew (Ospreys Academy), Andrew Bishop (Ospreys), Tom Riley (Blues Academy), Chris Czekaj (Cardiff Blues); David Flannigan (Blues Academy), Martin Roberts (Ospreys Academy); Rhys Gill (Blues Academy), Duane Goodfield (Blues Academy), Phil Osborne (Newport), Alun Wyn Jones (Ospreys Academy), Dominic Day (Scarlets Academy), Adam Powell (Blues Academy), Rhys Shellard (Blues Academy), Tom Smith (Ospreys Academy, capt).
Replacements: Ed Shervington (Neath), Craig Mitchell (Ospreys Academy), Will Jones (Dragons Academy), Ben Lewis (Ospreys Academy), Tom Cheeseman (Bath Rugby), Liam Davies (Scarlets Academy), Jamie Roberts (Blues Academy).
Wales Under-19s: Martyn Thomas (Scarlets); Alec Jenkins (Scarlets), Gareth Maule (Dragons), Jonathan Davies (Scarlets), Jimmy Norris (Dragons); Rhys Priestland (Scarlets), Darren Allinson (Scarlets); Hugh Gustafson (Scarlets, capt), Marc Jones (Exiles), Jamie Corsi (Dragons), Adam Brown (Dragons), James Down (Blues), Sam Kiley (Ospreys), Daniel Franks (Blues), Lewis Evans (Dragons).
Replacements (from): Keiron Jenkins (Blues), Nicholas Eaves (Blues), Bradley Davies (Blues), Ken Owens (Scarlets), Josh Turnbull (Scarlets), Ashley Smith (Dragons), Robert Lewis (Dragons), James Lewis (Dragons), Matthew Larsen (Blues), Marc Breeze (Ospreys).