Assefa was on track to break the women's marathon record until the 35-kilometre mark, when she slowed slightly and was clearly struggling with a leg injury.
The 29-year-old limped across the finish line and collapsed but still recorded 2:11:04, the third-best mark ever achieved by a woman over the distance.
The Ethiopian received medical treatment after the race and her manager Gianni Demadonna told Germany's NTV network on Monday she had undergone surgery for a torn Achilles.
"The pain started at the 31-kilometre mark, and from the 40th kilometre on, it became very intense," Demadonna, a former long-distance runner, confirmed.
"It is incredible how she managed to keep running and win the race despite that injury and pain. Now we have to wait and see how the surgery went."
Assefa, now a three-time winner in Berlin, switched from road racing to marathon running after a previous Achilles injury in 2016.
Demadonna said Assefa would miss around seven months but may be able to return for the London Marathon in April 2027.
