“He is ok now, scared but ok,” a Barcelona source told AFP, confirming press reports.
At least four men broke into his home in Castelldefels near Barcelona through the garden and threatened him and his wife with guns and iron bars, and hit him, daily El Pais reported.
The thieves fled by car after forcing the Gabon international to open a safe and making off with jewels that were inside, the newspaper reported.
A spokeswoman for Catalan police, the Mossos d’Esquadra, confirmed they were investigating a violent robbery in Castelldefels but refused to identify the victim, citing privacy rules.
“The investigation remains open and we are gathering information,” she told AFP.
The incident comes as Aubameyang is linked with a return to the Premier League after interest from Chelsea.
He joined Barcelona in February from Arsenal after reportedly having fallen out with Gunners manager, Mikel Arteta, due to disciplinary breaches.
Several high profile footballers in Spain have been subject to robberies, though most of these break-ins occur while the stars are playing.
In June, police arrested six people in connection with the three-million-euro burglary at the house belonging to former Brazil forward, Ronaldo.
Paris Saint-Germain player, Marco Verratti, was staying at Ronaldo’s house in Ibiza but was not home when the burglars struck, taking jewellery and money.
And earlier this month, police recovered Barcelona striker Robert Lewandowski’s watch, which was stolen as the player signed autographs before a training session.