The Ivorian was shown two yellow cards in the first half at the Liberty Stadium for challenges on Southampton defender Maya Yoshida.
Having clattered into the Japan international off the ball 20 minutes in, Bony was then dismissed following a dangerous tackle from behind.
While the hosts were resilient for much of the second half, Victor Wanyama's first Southampton goal proved crucial 10 minutes from time as Swansea slipped to back-to-back defeats in the Premier League.
However, Monk refused to be critical of his striker, who had been restored to the starting XI, and revealed the 25-year-old was hugely upset with his red card.
When Monk was asked about being disappointed with Bony's actions, the Swansea boss responded: "You could say that about most sendings off, of course. I don't need to tell Wilfried that, he was distraught in the changing room at half-time.
"He's a very good character and you make mistakes at times as players. I've done it myself, every player has made mistakes like that. Hopefully he'll learn from it and bounce back."
Swansea had dominated large spells of the first half, with Bony proving a handful prior to his dismissal.
However, with 10 men, the home side struggled as Southampton piled on the pressure before getting their reward courtesy of Wanyama's late winner.
Monk expressed his frustration at ultimately losing out, having kept the visitors at bay for much of the second half.
"We were so dominant in that first half and played some great stuff. It seemed only a matter of time before we were going to score and push on in the game," he added.
"We're disappointed with the goal because that's the one time we really switched off.
"Every single aspect, until the sending off, we dominated. I said to them at the end, if you continue to show everything you're doing and get better with it you'll have a very successful season."
