Video replays showed a pole-shaped object hitting Jordan on the head moments after Nabil Fekir had equalised for hosts Betis to draw the last 16 tie level at 1-1 at the Estadio Benito Villamarin.
"The match has been abandoned after Joan Jordan was hit by an object thrown from the stands. We'll provide you with further updates," Sevilla wrote on Twitter.
Alejandro Gomez put Sevilla in front in the 35th minute, but the lead lasted four minutes before Fekir's leveller.
Video replays showed that Jordan was struck from behind and collapsed to the ground holding his head, although reports said he was later able to stand while receiving medical attention. Referee Ricardo de Burgos Burgos wrote in his report that the object was a "hollow 50-centimeter (20-inch) PVC bar'' thrown from a zone filled with Betis fans.
The Spanish Football Federation (RFEF) announced that the game was suspended, adding: "The RFEF condemns any act of violence on the pitch."