Bothroyd had recovered from an arm injury and was set to play against the Spanish on the weekend but he was withdrawn just before kick off.
"Jay suffered an injury in the warm-up so we pulled him out of the team as a precaution," Jones said.
The boss is hopefull he will have the striker ready to face Sheffield Utd on Sunday.
"I think he will be alright," Jones continued.
"He cramped up and felt his hamstring when he was shooting before the game. So we'll pat him on the head and rub him down and hope he is okay."