Jade, Jesy, Perrie and Leigh-Anne beat Dua Lipa, Stormzy, George Ezra and Anne-Marie for the award at the ceremony in the Spanish city of Bilbao.
Camila Cabello honoured was the star of the show after she won Best Song, Best Video, Best Artist and Best US Act.
The ‘Havana’ singer, 21, beat Ariana Grande in several categories.
She said: ‘This has just been such an amazing year. Last year I performed in the EMAs and I was peeing myself.
‘I love my fans so much. I know what it’s like to be a fan. I know how special that bond is. I love you. I see you. I feel so lucky to even be here.’
Other winners included 89.7 Bay hitmakers Nicki Minaj, Shawn Mendes, Marshmello, Dua Lipa and Janet Jackson.
Winners of MTV EMAs 2018:
Best Artist – Camila Cabello
Best Song – Camila Cabello ‘Havana’
Best US Act – Camila Cabello
Best Electronic – Marshmello
Best Pop – Dua Lipa
Best Video – Camila Cabello ‘Havana’
Best Hip Hop – Nicki Minaj
Best New Artist – Cardi B
Best Rock Artist – 5 Seconds Of Summer
Best Live Artist – Shawn Mendes
Global Icon – Janet Jackson
Best UK and Ireland act – Little Mix