The hosts were poor from the off and their opponents were in the mood to punish them, taking a 1-0 lead in at the break thanks to Domi Kumbela's header.
Nothing changed after the interval, with Julius Biada able to double Braunschweig's advantage midway through the second period after a calamitous error from Sören Gonther.
Were it not for Robin Himmelmann, the home side would have been embarrassed in the scoreline as well as in the performance, the goalkeeper doing brilliantly to keep the score down.
However, that was merely a consolation, with the three points all Braunschweig's.
Setting the tone
After last weekend's loss to anticipated promotion rivals VfB Stuttgart, things didn't get off to the best of starts for St. Pauli in their home opener either.
Nik Omladic came within inches of giving Braunschweig the lead from a free-kick, his cheeky attempt hitting the near post, and then star defender Lasse Sobiech was subbed off through injury with only 11 minutes on the clock.
Phil Ofosu-Ayeh had the perfect chance to compound the hosts' misery on the 20 minute mark too, with Kumbela's cross inch-perfect, but the full-back's header was right at Himmelmann.
St. Pauli finally cave
This chance, which Braunschweig should have put away, looked to have acted as a wake-up call for the home side.
After Gustav Valsvik took the ball away from Aziz Bouhaddouz at the last second, Fafa Picault headed over from the resulting corner.
However, Omladic continued to be too hot to handle early on and was Braunschweig's creative spark in a strong opening half.
Centre-back Joseph Baffo missed an open goal from close range just before the half hour mark, albeit on the stretch, while Biada - the man who created that opportunity - came close himself moments later.
After spending 39 minutes knocking on the door though, Braunschweig would finally break the deadlock just before half time.
Baffo made up for his big miss by supplying the assist; a long ball aimed perfectly towards Kumbela, who took advantage of Himmelmann's questionable positioning to lob him with a cute header.
No change on the pitch - but a change in the scoreline
The sluggish St. Pauli that dragged themselves in at the break, dragged themselves back out for the second period with very little having changed.
Instead, the visitors were seeking a second goal, with Salim Khelifi not far away from giving them just that when his rasping shot fizzed just wide of the far post.
As the home side pushed on in search of an equaliser, they were leaving gaps at the back for Braunschweig to exploit too. However, it was not the allowing of this space that gave the away side that inevitable second half, but a horrible - and uncharacteristic - error from Gonther.
The centre-back, with plenty of time and space as his team knocked the ball around looking for an opening, stood on the ball and fell over, gifting possession to the lurking Biada.
The striker pounced and raced directly at goal, with nothing in his way and Himmelmann helpless as he slotted home with composure.
Himmelmann on hand to save further blushes
Braunschweig could smell blood and they went in for the kill, with Onel Hernandez and Omladic producing smart saves from the home 'keeper in quick succession.
Patrick Schönfeld came particularly close too, but Himmelmann was again there to save a defence falling apart before his very eyes with a strong stop.
Had it not been for the in-form stopper, it would have been a thrashing, but the blow dealt to St. Pauli by defeat will not be cushioned by that fact.