A number of O’s academy products were on show throughout the night, but Towell’s 16th minute effort from the edge of the box proved to be the deciding factor at the Amex Stadium.
The O’s made six changes from the side which bowed out of the FA Cup at Sheffield United on Sunday, with first starts handed to Zan Benedicic, Michael Collins and Josh Koroma, with the latter starting on the eve of his 18th birthday.
Orient also named a bench which consisted of seven players to have come through the club’s academy.
The first chance of the encounter fell the way of the academy side with Uwe Huenemeier heading a fifth minute corner into the side netting at the back post, before the O’s went up the other end and Sandro Semedo warmed the hands of Casper Ankergren.
Orient mounted another attack and Benedicic’s ball across found McCallum who saw his shot deflected behind for a corner as they began to settle into the game.
However, Brighton were able to break the deadlock on 16 minutes, punishing a midfield mix-up from the O’s.
Michael Collins played the ball into Benedicic, but Towell dispossessed the Slovenian and played in Elvis Manu. His shot looked destined for the net, only to be denied by a last-ditch Aron Pollock clearance as he clattered on to the post.
The danger wasn’t clear though and with Pollock laid low, Towell took a couple of touches before firing into the top corner past the outstretched dive of Alex Cisak in the O’s goal.
Chances had been few and far between in the opening stages but the hosts had the majority of the play and created the next opening when Seagulls skipper Will Collar found space down the O’s left before firing a right-footed shot just wide of the target.
Orient forced their second corner of the evening after a cross in from Janse found Semedo, only for his shot to be blocked behind by Tyler Hornby-Forbes.
As the half entered stoppage time the hosts mounted a quick counter-attack and the ball worked its way to Manu once more, however, Pollock was on hand to snuff out the danger as the hosts held the lead at the interval.
Victor Adeboyejo was brought on at the break for his first first-team minutes of the season in place of Simpson, while seven minutes into the half Jens Janse was forced off through injury and was replaced by Myles Judd.
Adeboyejo was heavily involved in the O’s first attack of the half and ended it when his shot was blocked behind for a corner, and the youngster continued to look bright, along with the likes of Judd and Koroma.
Kazenga LuaLua, a half-time substitute for the hosts, found space on the edge of the O’s box but saw his effort comfortably held by Cisak.
Chances were again at a premium in the second period, but O’s continued to look for a leveller and came close when McCallum got on the end of Kennedy’s fine corner, and that started a spell of pressure for the visitors.
Koroma then showed the Seagulls defence a clean pair of heels before seeing a shot well saved by the experienced Ankergren.
With just under 10 minutes remaining Henry Ochieng came on for his O’s debut in place of Benedicic, making it six O’s academy products ending the contest – a sign of the young talent at the club.
It was the O’s who ended the match on top, but try as they may, they were unable to force a late equaliser. Adeboyejo went the closest after the O’s won possession deep in the Brighton half but the effort from the striker was just off target.
Brighton & Hove Albion: Ankegren, Huenemeier (Hall 24), Manu, March, Towell (LuaLua HT), Starkey, Hutchinson, Hunt, White, Hornby-Forbes (Molumby HT), Collar.
Subs: Sanchez, Ward, Cox, Tilley.
Goals: Towell (16)
Orient: Cisak, Janse (Judd 52) , Dunne, Pollock, Kennedy, Koroma, Collins, Benedicic (Ochieng 81), Semedo, McCallum, Simpson (Adeboyejo HT)
Subs: Grainger, Dalby, Alzate, Clark.
Referee: Lee Probert.