Two goals from Omar Rowe and one from Corby Moore put the visitors in a commanding 3-0 lead going into half-time.
There was a mini resurgence from Albion as they managed to pull one back within a minute of the restart, and Saints were grateful to goalkeeper Cody Cropper for saving a penalty shortly before the visitors reasserted their dominance in the match. A strike from Harrison Reed and a peach of a volley from Jake Sinclair rounded off a confident performance.
After assistant Steve Greaves led a Saints XI to a 3-3 draw at Welling in midweek, coach Martin Hunter took back the reigns of the Development Squad for a match that had no senior players involved.
Cody Cropper kept his place in goal after an impressive 90 minutes against Welling United, while right-back Matt Young and left-back Matt Targett both started again.
Jack Stephens and Jordan Turnbull went straight in as the centre-back partnership having just returned from the pre-season tour with the First Team.
Reed was also called into the starting line-up after being rested for Tuesday's match away in south-east London, joining Dominic Gape and Moore in the middle of the park. Ryan Seager – scorer of two late goals against Welling – started up top with Sinclair and Rowe on either wing.
The visitors started the match brightly and looked to press Brighton at every opportunity to win the ball back quickly whenever they lost it.
In the first ten minutes, Albion barely made it out of their own half as chances for Moore, Seager and Rowe all went begging.
The deserved breakthrough goal arrived in the 12th minute for the visitors, though, as Gape played a crisp ball into the feet of ROWE, who took a touch and fired a left-footed shot past the 'keeper from 12 yards.
Saints doubled their lead four minutes later as Rowe and Targett linked up well down the left wing and the full-back's low cross found Seager, who teed up MOORE to drill a low shot into the bottom left corner.
The Seagulls were limited to few chances in the first 45 with Cropper left largely untroubled. Meanwhile, at the other end, Saints were peppering the goal – Sinclair crossed in for Gape who should have scored from point-blank range, but he was denied by a fantastic save from Christian Walton.
Before the half-time break, ROWE doubled his goal tally with an emphatic solo effort. A long jagged run in from the left touchline saw him skip past multiple challenges and, despite having his first shot blocked, with some quick footwork he managed to find half a yard and fire a low drive across goal and into the bottom corner.
HALF TIME: BRIGHTON U21S 0-3 SAINTS U21S
Brighton came out looking to press Saints in the same way that they had been in the first 45, and within 60 seconds they had got a goal back. Stephens sold short half-time substitute Joe Curtis and it was easy for Albion's trialist striker to run in and slot the ball past an out of position Cropper.
The home side started to build in confidence and shortly afterwards, they were awarded a penalty. George Barker got on the wrong side of Stephens, who tugged the shirt of his opponent inside the box. The fouled winger then stepped up to take the spot-kick, but was denied by an athletic diving save from Cropper down to his right.
The Saints stopper then further showed his worth by saving Courtney Richards' dipping 30-yard volley before being subbed off for Will Britt on 65 minutes.
Having weathered the early second-half storm from Brighton, Saints went back onto the offensive and it was REED who restored the three-goal lead. His right-footed shot from just outside the box took a strong deflection that lifted the ball over the keeper and into the back of the net.
Hunter then made his final substitution replacing Seager with Jake Flannigan, and it didn't take long for the switch to have an impact. Curtis released Flannigan down the right and the substitute cut the ball just behind the run of SINCLAIR, but the striker managed to flick the ball up in the air and over to his left side before rifling a volley past the 'keeper to round things off.
FULL TIME: BRIGHTON U21S 1-5 SAINTS U21S
"I was pleased particularly with the first half,” said Hunter post-match. “We created numerous chances and scored three good goals.
"When it went the 3-1 I had déja vu in my mind of West Brom (where Saints drew 3-3 last season having led 3-0) and then there was a really good save from Cody with the penalty.
"Things were very good in the first half and then the first 20 minutes of the second half we were sloppy to say the least.
"We've been doing a lot of work in pre-season. It was good to see the understanding of the young players and where they created the chances, and without being rude we could have scored seven goals in the first half.
"Their goal was poor, that was our mistake," Hunter added. "It's a poor pass that they've intercepted and Cody's out of the goal and that’s no reflection on him.
"That's not how you want to start a second half. It's maintaining the standards and consistency throughout the game. If they're going to be successful senior players then that's what they need to do."
Brighton U21s: Christian Walton, Bradley Barry, Trialist, Glen Rea, Trialist, Courtney Richards, Rohan Ince, George Backer, Brennan Dickenson, Trialist, Trialist.
Saints U21s: Cody Cropper (Will Britt 65), Matt Young, Jack Stephens, Jordan Turnbull, Matt Targett, Harrison Reed, Dominic Gape (Joe Curtis 46), Corby Moore, Omar Rowe, Jake Sinclair, Ryan Seager (Jake Flannigan 70). Unused substitutes: Fraser Colmer, Jason McCarthy, Jamal Branker