A strong hit from a tight angle courtesy of a trialist provided Southampton’s only goal on a night where chances were a rarity for either side.
The hosts effectively settled the encounter in the space of seven minutes with a low shot and a well-guided header in the first half.
Girona put the match beyond Saints in the 89th minute with a turn and cross that set up a looping header over substitute ‘keeper Nick Croucher that soared into the net.
After an uneventful start to proceedings, Girona threatened to get the breakthrough shortly before the quarter-hour mark when they rattled the crossbar with a glancing header from a corner.
Right on the half-hour mark, though, the home side’s persistence and pressuring saw them open the scoring.
A through-ball through the backline that looked destined to be recovered with ease, Colm Deasy was chased for the loose ball and his attempted clearance along the ground was prodded past James Needle at the near post.
Girona doubled their lead six minutes later when a cross was neatly headed back across the face of goal and directed in with another header in composed fashion.
Armani Little posed Saints’ greatest threat in the dying stages of the opening 45 minutes with a powerful free-kick whipped from an acute angle close to the corner, only to see it held at the near post.
The lack of opportunities after the restart mirrored the style of the first period, with coach Anthony Limbrick filtering substitutes through as the half progressed.
It was one of those replacements – a trialist – that pulled a goal back for Southampton with just under 20 minutes remaining.
The youngster snatched possession in the left side of the box and slammed a perfectly-hit drive past the ‘keeper and into the side-netting in the far corner.
As Saints poured forward in search of a leveller, the hosts troubled on the break in the 76th minute but a shot towards the near post was well-held by substitute custodian Croucher.
He could do little to prevent Girona’s third with a minute left when a swift turn and cross from the left was nodded over Croucher and into a gaping net.
Southampton U18s: James Needle (Nick Croucher 46), Colm Deasy (Ben Cull 55), Ollie Cook, Josh Debayo, trialist (trialist 64), Alfie Jones, Armani Little (Joe Lea 74), Stuart Wilkin (Carel Kayembe 49), Harley Willard (Mark Irvine 46), Dan Demkiv (trialist 64), Marcus Barnes (trialist 68). Unused substitutes: Richard Bakary.