Aubameyang was assaulted in the early hours of Monday morning when a gang broke into his home equipped with firearms and iron bars.
Club sources initially said Aubameyang and his wife -- who were handcuffed during the burglary with their kids also inside the property in Castelldefels, just outside of Barcelona -- did not have serious injuries.
But sources have now confirmed to ESPN that the former Arsenal striker did break his jaw during the break-in and will be out for around three weeks, which could have implications on a proposed move to Chelsea.
Aubameyang later confirmed the news on social media in a post that read: "Hey guys, thanks a lot for all the messages. On Sunday night, some violent cowards broke into our home and threatened my family and my children, just to steal some stuff.
"They injured my jaw but I will recover in no time, and thank God no one else was physically harmed. The feeling that we are no longer safe in our own home is hard to understand and describe, but as a family, we will overcome this and stronger than ever. Thanks for all the support, it really means a lot to us. Auba."
Barca and Chelsea held talks on Tuesday over a deal for Aubameyang and will meet again on Wednesday to discuss a possible transfer.
The Premier League side have made it clear from the start they do not want to pay over €20 million for the forward, while Barca were initially holding out for more than €25m.
The injury to Aubameyang's jaw has slightly changed the negotiations, however, with a loan to the west London club emerging as a possible solution.
Barca coach Xavi Hernandez is happy to keep Aubameyang, but the club's need to reduce their wage bill to fund other business before the transfer window closes this week has forced them to listen to offers.