The Bundesliga club are flying with the 21-year-old spearheading their attack, now inside the top-four with a four-point gap to their nearest rivals - and qualifying for the Champions League is Jovic's top priority.
Goncalo Paciencia and Luka Jovic got the goals for the visitors.
Adi Hutter's side are likely to activate their purchase option at the end of Jovic's two-year loan deal from Benfica before then assessing offers from prestigious clubs across the continent.
Jovic himself has said that he would be open to staying at Frankfurt if the team make it into Europe's top competition.
"But he's not interested at this time".
"He wants to continue in the Bundesliga and qualify for the Champions League with Eintracht. I want to play football".
"He was here a few days ago and said, 'Dad, I'm not anxious about money".
Eintracht are fourth in the Bundesliga with a four-point cushion to Borussia Monchengladbach in the race for Champions League football.
Luka Jovic levelled for the German side, but Felix's second and Ruben Dias' header put Benfica in control.
The wonderkid has been something of a sensation in his first full season as part of the Benfica senior squad, scoring 10 league goals in just 18 appearances for the Primeira Liga leaders (albeit on goal difference), and has now taken his goalscoring exploits to the Europa League.