The ITV star decided to try and intervene after the duo made a series of cutting digs at each other.
Susanna, 49, admitted she was so surprised she thought a clash had occurred at the morning meeting.
Susanna said: "Have you two had a tiff off air?
"It feels like there is something brewing, did I miss something?
"Now you two calm down."
Returning after a short break, Susanna went on to reveal how Charlotte had lost it behind the scenes.
Susanna said: "I do wonder what happened to Charlotte Hawkins.
"She threw her script in the break."
Shrugging it off, the blonde babe replied: "If only my throw had been better.
"I did actually need those notes so I had to go and get them."
GMB bosses then played a clip of a sheepish Charlotte walking over and picking up her stack of papers.
Turning to Piers, Charlotte added: "You're on one of those missions to antagonise me."
Laughing, the former newspaper editor hit back: "I didn't get much sleep last night.
"I had this weird cheese last night and it gave me funny dreams."
Taking to Twitter to comment on the clash, one GMB viewer commented: "Charlotte and Piers Morgan are like squabbling siblings."
Another added: "Haha Piers Morgan brightens my day up... love him #GMB."
Meanwhile, a third continued: "Charlotte Hawkins and Susanna Reid are Goddess like.
"Their levels of toleration are on a whole other level. How they put up with Piers Morgans patter on a daily basis is beyond me. Hats off ladies."
A fourth joked: "Charlotte is gonna batter piers #newsgate."
Good Morning Britain airs weekdays on ITV at 6am