After taking a third-minute lead through a typically composed finish courtesy of Ryan Seager, the visitors were unlucky not to double their lead when Gallagher sent a rising drive crashing off the crossbar.
The Blues responded well immediately after the woodwork was rattled when they stole possession and struck through Chris Long before preventing Saints from grabbing the lead back when Mateusz Taudul saved Jake Sinclair’s penalty.
Two converted spot-kicks by Luke Garbutt shortly after the break ultimately sealed the defeat for Saints after Sinclair’s tackle and Sam McQueen’s handball gifted Everton the opportunity to take all three points.
Any anxiety caused by Harrison Reed requiring treatment inside the first ten seconds was soon dashed in the third minute when SEAGER calmly sent Saints into the lead.
Gallagher deftly flicked a Matt Targett pass into the path of his fellow forward for a side-footed effort into the bottom corner from the edge of the area.
The Blues responded well and threatened through a goalmouth scramble ten minutes later as Long came close to prodding in before Saints frantically cleared for a corner.
Long’s partner Magaye Gueye was hesitant in his forays as he found space through Saints’ backline in the 17th minute but elected to try and pull the ball back, scuffing his attempt in the process and allowing a clearance.
Long was audacious in his efforts shortly after when he turned Jordan Turnbull down the right flank and hit an unlikely shot that was caught at the near post.
Everton’s striking pair proved to be influential in first-half affairs as they combined immediately after the hosts stole possession deep in Saints’ defence; Gueye dithered on the ball in the box before playing it across to Long for a shot that deflected wide.
After Gallagher had teed up Seager for the opener, the latter returned the favour in the 24th minute when he held up the ball and laid it into the path of the onrushing Gallagher who agonisingly rattled the crossbar with a chopped strike.
Southampton were made to rue not fashioning a two-goal margin moments later when they were caught out in their own box.
LONG snatched possession near the byline before accurately tucking the ball in from an acute angle to level matters.
With just over ten minutes remaining in the half, Saints were handed a golden opportunity to re-establish a lead when Tyias Browning blatantly slid Gallagher to the ground.
Sinclair assumed the spot-kick duties but was denied as Mateusz guessed correctly with the direction of his dive and palmed away.
Gallagher continued to be a nuisance for the Blues’ rearguard as half-time approached when he burst into the box beyond several challenges and fired towards the near corner, only to be thwarted by the hand of Taudul pushing the ball around the post.
HALF-TIME: EVERTON U21s 1-1 SOUTHAMPTON U21s
A disastrous restart for Saints ensued after the break when the retreating Sinclair’s momentum saw him unfortunately chop Long down in the box for a penalty.
Everton’s dedicated set-piece taker GARBUTT stepped up to calmly slot into the bottom-left corner from 12 yards to hand Everton the lead for the first time in the encounter.
The leaders were awarded another penalty eight minutes later when McQueen accidentally handled a cross in the box, allowing GARBUTT to opt for the other corner with a penalty that squirmed in.
Saints refused to back down; Targett whipped in a dangerous cross that flashed across the face of goal but unfortunately drew no contact from the onrushing Seager and Gallagher.
Everton remained a troubling proposition on the break amidst Southampton’s growing pressure, Conor Grant’s side-footed volley wide at the near post from George Green’s cross providing a worrying moment for the visitors.
Sadly, Saints couldn’t make their pressing count as Everton stayed sturdy and restricted the visitors to very little joy in the final third, ensuring the score was unchanged late on.
FULL-TIME: EVERTON U21s 3-1 SOUTHAMPTON U21s
Everton U21s: Mateusz Taudul, Gethin Jones, Luke Garbutt, Tom Davies (Calum Dyson 68), Tyias Browning, Curtis Langton, Conor Grant, Joe Williams, Chris Long, Magaye Gueye (Courtney Duffus 79), George Green. Unused substitutes: Russell Griffiths, Ibou Touray, Ben McLaughlin.
Southampton U21s: Ted Smith, Matt Young, Matt Targett, Dominic Gape (Jake Flannigan 68), Jason McCarthy, Jordan Turnbull, Jake Sinclair (Omar Rowe 46), Harrison Reed, Sam Gallagher, Ryan Seager, Sam McQueen (Jake Hesketh 68). Unused substitutes: Niall Mason, Chris Johns.