The England wing has been charged with a "lifting tackle" on the Barbarians centre Berrick Barnes at Bluetongue Stadium in Gosford and was due to face a disciplinary hearing in Sydney overnight.
England have now had a player cited after all three of their matches on the tour of Australia.
Lock Dave Attwood had two stamping charges thrown out following the 28-28 draw with the Barbarians and wing Mark Cueto was found not guilty of a dangerous tackle on Barnes in Saturday's Test defeat to the Wallabies.
Banahan is unlikely to be involved in this weekend's second Test anyway but a guilty verdict could officially rule him out of the game in Sydney and England's final tour match against the New Zealand Maori next week.
Martin Johnson put a brave face on another flawed performance after England scraped to their first victory of the tour.
Two penalties from Charlie Hodgson and three from Olly Barkley were eventually enough to see off the Australian Barbarians 15-9.
England had started well but lost their way and were forced to use attack coach Brian Smith as a water-carrier to pass on tactical instructions after the Barbarians edged into a 9-6 lead.
Australia's second-string ended up with two hookers in the front row and England's scrum milked their good fortune as Barkley's boot sealed the win.
"It was a pretty ugly contest. The sooner we move on, the better," said Australia's head coach Robbie Deans.
But after the 28-28 draw with the Barbarians and the 27-17 first Test defeat to the Wallabies, Johnson welcomed the victory as a boost to the tour.
"At times we played well. We have won in Australia. Our second string have played their second-string twice and we have got a draw and a win," said Johnson. "You can't substitute winning, you can't fake it. That is what we are here to try and do.
"Am I saying it was fantastic? No. There are some things we can do better but we were three points down away from home in difficult conditions and we won by six."
England's Test players remained in Sydney and did not make the 50-mile journey north to Gosford after Johnson decided the trip would be too arduous following their "intense" training run yesterday morning.
Mike Tindall limped out of the session with a dead leg but Johnson insisted he is confident the centre will be fit to start at Stadium Australia on Saturday.