The accolade was one of six won by the BBC serial at the magazine's 15th consecutive awards ceremony. ITV's Coronation Street took home four awards, while Emmerdale and Neighbours nabbed two each.
Lacey Turner's portrayal of Albert Square's widowed mum Stacey Branning won her the title of 'Best Actress' for the fifth year in a row. Her former on-screen husband, played by Charlie Clements, scooped 'Best Exit', after falling to his death during the show's live episode earlier this year.
Emmerdale's Danny Miller was named 'Best Actor', while the episode which saw troubled teenager Aaron Livesy admit that he is gay to Paddy Kirk, won Miller his second award of the night for 'Best Dramatic Performance'.
'Enders star Scott Maslen (Jack Branning) picked up 'Sexiest Male', and Corrie's Michelle Keegan (Tina McIntyre) landed the 'Sexiest Female' award for the second year in a row. Her on-screen boyfriend Craig Gazey took home 'Funniest Performance' for his role as Graeme Proctor.
Speaking about his win, Gazey said: "It's a great honour to follow in the footsteps of last year's winner, the incredible Maggie Jones. Thank you to everyone who voted for me. The fact it's an award from viewers is very special.
"I keep my 'Best Newcomer' Inside Soap Award in the bathroom so that's where this one will be going!"
Coronation Street's Alex Bain (Simon Barlow) won 'Best Young Actor' for a second time, while the dramatic scenes which saw Tony Gordon escape from prison and blow up the Underworld factory landed 'Best Stunt'. Alison King, who plays Carla Connor, commented: "The factory fire scenes were some of the hardest I've ever done, they took four weeks to film and we were working with fire, which was especially dangerous."
She continued: "By the end of it all we felt like a little family though. Everyone worked so hard and they definitely deserve to win something. So thank you so much Inside Soap!"
Adding to EastEnders' total were the 'Best Newcomer' award for Ricky Norwood (Arthur 'Fatboy' Chubb) and 'Best Wedding'.
Meanwhile, Neighbours was crowned 'Best Daytime Soap', while the Australian soap's Ryan Moloney (Toadie Rebecchi) scooped 'Best Daytime Star'.
Waterloo Road was awarded the 'Best Drama' prize.
Steven Murphy, the editor of Inside Soap, said of the results: "With EastEnders' 25th anniversary and Corrie's approaching 50th, it's been a blockbuster year for soaps. Meanwhile, Emmerdale has come out fighting with some fantastic storylines and performances. It's wonderful to be able to reward the amazing work we've seen this year."
This year's ceremony was held at Shaka Zulu in Camden, London.
Check back on DS tomorrow for full video coverage from the awards.