Boey came on in the ninth minute after regular right-back Konrad Laimer was forced off following a blow to the foot, and performed solidly in Bayern's 3-1 victory.
Eberl addressed the situation afterwards.
"There's no question that Sacha has qualities. Yes, injuries could change the situation, but keeping Sacha just because Konny is out for a week would be wrong, both financially and from a footballing perspective," Eberl said.
Bayern Munich have already made clear they are no longer planning around the 25-year-old, who joined for a reported €30million and is regarded as a flop at the club despite a contract running until 2028.
He spent the second half of last season on loan at Galatasaray, and Bayern would still prefer to sell him outright this summer, though concrete offers have so far failed to materialise. João Palhinha and Bryan Zaragoza are in a similar position, with the club also open to selling both this window.
Elsewhere in Munich, promising 19-year-old Felipe Chávez is set for another loan spell after impressing during pre-season with two goals and two assists in a friendly against Rottach-Egern and an opener against Jeju SK.
According to Sky Germany, newly promoted SC Paderborn, second-division side VfL Wolfsburg, LaLiga club Deportivo A Coruña and an unnamed Portuguese top-flight side have all shown interest in the Peru international.
Chávez previously spent the second half of last season on loan at 1. FC Köln, making just seven appearances, and his contract at Bayern runs until 2028.