Braehmer, 36, was made to work in the fourth defence of his title but after landing a barrage of heavy blows in the ninth the fight was waved off as his fellow German attempted to come out for the 10th.
After a cagey opening round Krasniqi managed to catch Braehmer with a crisp left hook in the second but the champion soaked up the punishment and replied with a southpaw left which backed the challenger up onto the ropes.
Braehmer went for power in the third round as he tried to land heavy blows, but Krasniqi weathered the storm and switched his attack to the body in the next.
A short left from Braehmer shook the challenger in the fifth round and appeared to shift the fight in his favour.
Krasniqi was wobbled again by a left in the sixth but he continued to fight on the front foot and caught Braehmer with a right hook to the head.
Braehmer replied with a short left at the start of the eighth and had Krasniqi in trouble again later in the round with a left to the head but the challenger hung on and regained his senses.
Another heavy left sent Krasniqi sprawling onto the ropes in the ninth which prompted the referee to intervene with a standing count and the 26-year-old survived another onslaught before hearing the bell.
However, the attack left Krasniqi with a nasty cut lip and after inspection by the ring doctor and referee the fight was officially stopped one second into the 10th round.
Victory saw Braehmer extend his record to 46-2 (34 KO), while Krasniqi slipped to his fourth defeat as he was stopped for the first time in 47 contests.