Jake Sinclair struck twice inside the first half on a chilly Good Friday evening at Eastleigh's Silverlake Stadium with a young Saints side good value for their three points.
U21 Coach Martin Hunter had made five changes to the side that was disappointingly beaten two-nil at Arsenal 18 days earlier.
Out went overage players Vegard Forren, Steve De Ridder and Danny Butterfield, while Matt Young dropped to the bench and Andy Robinson was absent altogether.
Dominic Gape and Harrison Reed – regulars for Southampton's Under-18s this season – came in for their first starts in the Barclays U21 Premier League.
Also recalled was left-back Matt Targett, who missed the Arsenal game through injury, while Lloyd Isgrove and Jordan Turnbull stepped back into the starting line-up.
Paulo Gazzaniga kept his place in goal despite Cody Cropper's return to the squad, with Targett and Turnbull joined in defence by skipper Jack Stephens and right-back Calum Chambers.
Corby Moore completed a three-man midfield along with Gape and Reed, while Jack Sinclair and Omar Rowe joined Isgrove in attack.
With First Team Manager Mauricio Pochettino watching on, Saints started brightly and forcing a corner inside the opening 15 seconds thanks to some good work down the right by Isgrove.
It was down the same flank that the hosts had more success soon afterwards, when Chambers set Rowe free only for the winger to shoot over after cutting onto his left.
After a frantic opening, the game rapidly settled down as both sides found their feet on a chilly evening in Eastleigh.
The deadlock was broken on 18 minutes when some good play on the edge of the Wolves box allowed Gape to play in SINCLAIR, and the striker bundled the ball past goalkeeper Aljaz Cotman to make it one-nil.
Saints could well have added a second four minutes later when Isgrove got clear of left-back James Reckord after picking up Reed's long ball but his low ball was diverted inches wide of the far post.
Gazzaniga was untested until the 30th minutes, when some direct play by Wolves saw the ball find David Moli at the far post but his shot was easily held.
And it was the Argentinian goalkeeper who played a key role in Saints' second. After collecting a loose ball, he quickly found Targett with a superb kick and the ball made its way to SINCLAIR via Moore, with the frontman finishing excellently with 33 on the clock.
Wolves came back strongly, with Sam Winnall going close five minutes before the break with a fierce cross-cum-shot that Gazzaniga was forced to tip over.
There was a hairy moment for the Saints stopper soon afterwards, though, when he looked to claim a low pass under pressure only for the ball to squirm out of his grasp, but Stephens was on hand to hack clear.
HALF TIME: SAINTS U21S 2-0 WOLVES U21S
Hunter's team emerged from the break keen to avoid a repeat of the return fixture at Molineux, where they led by the same margin only to end up drawing two-all.
It took until after the hour mark for the first chance of the second period, with some sloppy play in the Saints midfield allowing Sam Winnall to get clear only goal only to shoot well over Gazzaniga's bar.
Wolves midfielder Lee Evans then flashed a low shot just wide of the right post as Wolves looked to chip away at the hosts' two-goal lead with no avail.
Gazzaniga then did well to tip over from Winnall with 72 minutes on the clock after he'd been played in well by Robbie Parry.
Those half-chances aside, Saints generally controlled the game with their midfield trio of Reed, Moore and Gape imposing themselves on their opponents well.
Saints' first real chance of the half arrived ten minutes from time when Targett surged forward and whipped over an excellent cross that was just beyond the head of substitute Sam McQueen.
Isgrove was even closer to rounding off the result a minute from time when he fired at goal on the turn but his shot came back off the post and into Cotman's grasp.
In the end, Saints were good value for their two-goal winning margin as they moved up the Elite Group standing as they enter the run-in.
Saints U21s: Gazzaniga, Chambers, Stephens (c), Turnbull, Targett, Gape, Reed, Moore, Isgrove, Sinclair (McQueen 80), Rowe. Subs (not used): Cropper (GK), Curtis, Young, Ariyibi.
Goals: Sinclair (18 & 33)
Wolves U21s: Cotman, Whittall, Reckord, Evans, Tank (Iorfa 69), Ihiekwe (c), Parry, Price (Kellerman 76), Moli (Jakobsson 66), Winnall, Cranston. Subs (not used): Flatt (GK), McAlinden.
Referee: David Rock