Flores’ assistant Tshegofatso Mashego has also been shown the door at the club.
Eagles announced the duo’s dismissal on their official Facebook account.
“Super Eagles have amicably parted ways with head coach Antonio Jesus Flores and assistant coach Mashego Tshegofatso after a string of poor results.
“The new coach will be announced in due course,” read the club statement.
Flores joined Eagles in November last year. He replaced Mashego, who was demoted to the assistant coach role following a poor start to the season that saw the team winning just two of their first 10 league matches.