Joe Pigott and Kwesi Appiah were on target for the Dons, while Brighton replied through a Oliver Norwood penalty in the second half.
New signing David Button made his debut in goal, while Shane Duffy also featured for the first time in pre-season after groin surgery but he went off after just 22 minutes and striker Jurgen Locadia limped off just before the hour.
Bruno, Lewis Dunk, Bernardo, Davy Propper, Markus Suttner and Tomer Hemed were not in the squad as they were among those who played in the 3-0 hour-long friendly win against Crawley yesterday.
Albion went close to opening the scoring on nine minutes as Jurden as Locadia raced on to Dale Stephens' pass but his shot was pushed behind for a corner by keeper Tom King.
Just a minute later, the hosts threatened as Appiah skipped clear past Duffy but saw his goalbound shot blocked by Ben Barclay, when a square pass to team-mate Pigott might have been the better option.
The Dons took the lead on 15 minutes as Liam Trotter headed a half-cleared cross back into the penalty area and Pigott span past his man before firing home low into the bottom corner.
Locadia blazed over from the edge of the penalty area on 21 minutes, before Duffy went off shortly afterwards.
Wimbledon went 2-0 up on 31 minutes. Mitchell Pinnock's cross from the left was headed down by Pigott and Appiah poked home from close range.
Albion's club record signing Locadia had another opening on 35 minutes but King again came out on top as the Dons stopper kept out the Dutch striker's low drive.
King then kept out Anthony Knockaert's close-range, before Locadia sent a left-footed effort wide after he got through one-on-one.
The Seagulls made a lively start to the second half and almost got a goal back on 50 minutes when Locadia fed Knockaert but the French winger's curling effort from 20 yards came back off the far post.
Locadia immediately signalled to the Albion bench after going down under a challenge with Will Nightingale on 58 minutes and went straight into the changing room as youngster Aaron Connolly replaced him.
Brighton got a goal back seven minutes later as Connolly went down under a Nightingale challenge and Oliver Norwood sent King the wrong way from the resulting penalty.
King pushed away Richie Towell's fierce strike on 68 minutes, before Wimbledon's Anthony Wordsworth sent a low drive just wide on 72 minutes.
Albion - with a young side on the field after a host of substitutions - pressed for an equaliser as Connolly inparticular looked lively but Wimbledon held on to win.
Brighton had drawn their opening friendly 1-1 away to Swiss side St Gallen last week, while this was Wimbledon's fourth pre-season friendly. Their latest outing was a late 1-0 defeat to Queens Park Rangers, after victories over Reading (4-2) and Woking (3-1).
AFC Wimbledon: King; Watson, Nightingale, Oshilaja, Meades, Pinnock, Hartigan, Trotter, Wagstaff, Pigott, Appiah. Subs: McDonnell, Sibbick, Thomas, Soares, Barcham.
Albion: Button; Schelotto (Moore 71), Duffy (White 21), Barclay, Bong (Davies 71); Knockaert (Tilley 71), Kayal (Mandriou 71), Stephens (Norwood 61), March (Gyokeres 71); Gross (Towell 61); Locadia (Connolly 58). Subs: McGill.