Police took a 74-year-old home supporter into custody after viewing televised footage of the incident, which occurred 26 minutes into the League Two clash.
The man has since been released on bail as his actions are not believed to have been racially motivated.
"We saw the banana thrown onto the pitch and then reviewed television coverage," football intelligence officer Sam Cunningham told This Is Staffordshire.
"It appears a supporter was angered by a decision by the referee and aimed a banana at him. It was not aimed anywhere near any player."