Alexandre Lacazette marked his 100th Gunners appearance by heading his side level after Adam Webster had given the visitors a first-half lead.
With the score 1-1, there was frustration for Ljungberg and Arsenal when David Luiz thought he had made it 2-1 with a volley but it was correctly ruled out following a VAR check for offside.
Neal Maupay headed Brighton’s winner from Aaron Mooy’s cross to leave Arsenal on their worst winless run since 1977 – and 10 points off a Champions League spot.
Where do Arsenal go from here?
Arsenal, who are 10th in the table, have now failed to win any of their last nine games in all competitions and fans who stayed for the final whistle booed their team off the pitch after a tepid performance.
Twelve years after his last appearance for Arsenal as a player, Ljungberg was given a chance to show fans inside a far-from-full Emirates he is capable of managing the club where he won two Premier League titles and three FA Cups.
It started well, with the Swede given a decent reception by the crowd, before rapidly going downhill as Brighton, who had lost their previous four away games, took control.
Ljungberg dropped Shkodran Mustafi from his 18 after last Sunday’s 2-2 draw with struggling Norwich, yet Arsenal were still a shambles at the back.
Maupay had already forced Bernd Leno into a one-handed save when Webster struck from a corner after lashing home following Dan Burn’s downward header.
Arsenal improved with the introduction of club record signing Nicolas Pepe after half-time and France forward Lacazette lifted the mood by climbing above the Brighton defence to head his side level after Mesut Ozil’s first Premier League assist since February.
Yet the Gunners were short on confidence and ideas – while Mat Ryan produced a superb save at the end to frustrate the home side further.
The Brighton keeper flung himself across his line to keep out substitute Gabriel Martinelli as Arsenal, who have home games against Manchester City, Chelsea and Manchester United on the horizon, failed to win for the 11th time in 15 top-flight attempts.
The home side’s night was summed up towards the end of the first half when Pierre-Emerick Aubameyang had a go at team-mate Joe Willock after a home move had broken down.
More Emirates joy for Potter
Brighton boss Graham Potter was making his first return to Arsenal since his Ostersunds team beat the Gunners in the Europa League in February 2018.
Asked before the game whether he would be a Premier League manager if Ostersunds had not had a good run in Europe, Potter said: “Probably not. We all get to a certain point by doing something and everyone’s path is different. Ostersunds was mine.”
The Seagulls had given leaders Liverpool a late score on Saturday and, on a night to remember, they carried on from where they left off at Anfield to climb three places up the table to 13th – one point behind Arsenal.
Brighton’s first Premier League win since 2 November was built on guts and determination.
While Maupay, who now has five goals this season, and 19-year-old Aaron Connolly tormented lacklustre Arsenal, Webster and Dunk were solid at the back for the visitors.
In addition, Potter’s arrival at Brighton has seen them become a menace at set-pieces.
Seven of Brighton’s last 10 league goals have been scored via set-piece situations.
Man of the match – Mat Ryan (Brighton)
‘This is not Arsenal’ – what they said
Arsenal interim boss Freddie Ljungberg: “We didn’t show up in the first half, didn’t work hard and want to play.
“Second half we had a word and were better but we are suspect on the counter and we have no confidence. I need to work on that and get confidence back into the boys.
“At half-time we said ‘This is not Arsenal, we have to give it a crack.’
“We’re in a difficult situation, we’ve lost a lot of games and the confidence has gone down.”
Brighton boss Graham Potter: “It’s a nice moment for us. It gives us a little bit of belief. It was a good game for us, not perfect but we showed real courage and belief.
“Credit to our players, they did what I think an away team has to do in terms of frustrating but it still takes courage from the players and that’s what I’m pleased with.
“We dug in, I’m very pleased.”
Miserable times at Arsenal – the stats
- Arsenal have faced 52 shots on target in Premier League home games this season – in the entire Invincibles season in 2003-04, they allowed just 48 opposition shots on target at home.
- Including caretakers, only one of Arsenal’s last five managers has won their first home game in charge – Pat Rice against Sheffield Wednesday in September 1996.
- Brighton have beaten ‘big six’ opposition away from home in the Premier League for the very first time at the 17th attempt; they had lost 15 of the previous 16 such games.
- Arsenal’s Alexandre Lacazette has scored 25 of his 32 Premier League goals at the Emirates Stadium.
- Brighton ended a six-match winless run away from home in the Premier League this season.
Arsenal do not play again until Monday when they visit West Ham (20:00 GMT) in a London derby while Brighton are in action on Sunday when they host in-form Wolves (16:30 GMT).