The pop megastar approached the boys as they were being filmed backstage at the event in Brooklyn, NYC, last night - and their chat and subsequent group hug was caught on camera.
The fivesome had got a rough reception as they collected their Song Of The Summer award for Best Song Ever, which their huge fanbase had helped them secure with a tsunami of online votes.
Still wearing her Venus costume, GaGa told them: "Don't you dare let those people boo you.
"If I did hear what I heard out there, I just want to tell you that you deserve every bit of success that you have."
Telling them she had also been booed, she claimed that she had wanted to say something about it.
"I want to leave right now. I don't want to stay anymore because I don't want to be in a room where people are booing."
But the boys brushed the episode off, with Liam Payne saying: "F**k it, f**k it."
They then joined together for a group hug and to pose for photos.
The 2013 MTV Video Awards will be shown on MTV from 8pm on Monday August 26.
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