The ITV soap was also awarded for 'Best Shock Twist' – Val's gruesome death in the hall of mirrors – while actors Amelia Flanagan (April Windsor), Ryan Hawley (Robert Sugden) and Danny Miller (Aaron Dingle) also took home gongs for their work.
Overall it was EastEnders that won the most prizes, adding another five Inside Soap Awards to the mantelpiece including 'Best Exit' for Dame Barbara Windsor's departure as Peggy Mitchell.
Dame Barbara said: "I was nervous [about saying goodbye to Peggy], of course I was. But Peggy's exit was wonderful – I really couldn't have asked for more. The writers spoilt me, they really did!"
Meanwhile, Jacqueline Jossa scored 'Sexiest Female' as Lauren Branning, and Steve McFadden (Phil Mitchell) and Lacey Turner (Stacey Fowler) took the 'Best Actor' and 'Best Actress' awards. Tameka Empson won 'Funniest Female' for a fifth time thanks to her role of Kim Fox-Hubbard.
Elsewhere, there was a first-ever Inside Soap win for Holby City which triumphed in the brand new category 'Best Drama Storyline' for Arthur's death.
Another new category was 'Best Drama Star' which went to Casualty's Derek Thompson, who has played Charlie Fairhead for 30 years.
Popstar Shayne Ward, meanwhile, took home 'Best Newcomer' for his character Aidan Connor in Coronation Street, making it his third award in recent months after having won a the National Television Awards and TV Choice Award this year as well.
"I've been blessed to have such great storylines in the first year that I've been here," said Shayne. "This just rounds it off. It's been a great year and this is the cherry on top!"
The awards were handed out on Monday, 3 October at London's historic Hippodrome.
THE FULL WINNERS' LIST
Steve McFadden (Phil Mitchell, EastEnders)
Lacey Turner (Stacey Fowler, EastEnders)
Best Bad Girl
Persephone Swales-Dawson (Nico Bradley, Hollyoaks)
Best Bad Boy
Connor McIntyre (Pat Phelan, Coronation Street)
Tameka Empson (Kim Fox-Hubbard, EastEnders)
Joe Duttine (Tim Metcalfe, Coronation Street)
Shayne Ward (Aidan Connor, Coronation Street)
Best Young Actor
Amelia Flanagan (April Windsor, Emmerdale)
Charlie Clapham (Freddie Roscoe, Hollyoaks)
Jacqueline Jossa (Lauren Branning, EastEnders)
Ryan Hawley & Danny Miller (Robert Sugden & Aaron Dingle, Emmerdale)
The live episode (Coronation Street)
Best Shock Twist
Val dies in the hall of mirrors! (Emmerdale)
Barbara Windsor (Peggy Mitchell, EastEnders)
Best Drama Star
Derek Thompson (Charlie Fairhead, Casualty)
Best Drama Storyline
Arthur's death (Holby City)
Best Daytime Star
Alan Fletcher (Karl Kennedy, Neighbours)
Best Daytime Soap
Steven Murphy, editor of Inside Soap, said: "It's been a dramatic year in soapland with some stand-out plots and amazing performances, so the competition was tougher than ever. However, if anyone can make the right decision, it's the readers of Inside Soap magazine – Britain's original and best TV soap weekly."