The Channel 4 drama claimed three prizes in the public voting, pulling ahead of EastEnders and Emmerdale, which secured two gongs each.
Hollyoaks favourites Emmett Scanlan and Kieron Richardson were among the winners, picking up the 'Forbidden Lovers' award for their portrayal of Brendan Brady and Ste Hay's intense relationship.
News of the pair's success comes just as viewers have seen Scanlan's dramatic final scenes in the role of Brendan this week.
Speaking of the triumph, Scanlan commented: "It's just incredible. Out of all my awards, this was the one I was most confident about because I know how hardcore the Stendan fans are. It's nice to have this trophy too, because this is the final chapter.
"Their bond was destructive at times, but in Steven, Brendan found true love. The feelings were so strong - Brendan even killed for him. They certainly weren't your conventional couple, but who is?"
Richardson added: "If I could snog every single person who voted for us I would! We're chuffed that people have taken Ste and Brendan into their hearts."
Hollyoaks also won the 'Best Stunt' trophy for the wedding day bus crash and the 'Best Storyline' title for Esther Bloom's tragic bullying ordeal.
Jazmine Franks, who plays Esther, said: "We all worked so hard, so to get this recognition is great. I'm so grateful to everyone who voted, and it makes it even more special that the viewers are behind Esther."
Meanwhile, EastEnders was successful in the 'Best Reveal' category as the unexpected arrival of Max's secret wife Kirsty (Kierston Wareing) proved popular with voters.
Jake Wood, who plays Max, enthused: "We're both absolutely over the moon - I'm thrilled for Kierston as it's her first award. I'd known what Max's secret was going to be for over a year, so I'm just pleased it's out in the open now and I can relax!"
Walford's second winner was the ongoing Lola and Lexi storyline, which was named 'Best Baby Drama'.
Emmerdale picked up the 'Best Episode' award for its hour-long 40th anniversary live edition, while Carl King's shock murder in the special broadcast was named 'Best Death'.
Finally, Coronation Street also earned a prize as Kirsty and Tyrone's nuptials triumphed in the 'Best Wedding' voting.
The next issue of All About Soap, which goes on sale on Tuesday (March 26), will celebrate the results with exclusive pictures and interviews with the winners.
Photo gallery - a selection of winners with their All About Soap Awards.
"Hollyoaks scored the most wins with prizes for the ever-popular Brendan Brady, who bowed out on screen this week, the much-talked-about cyber bullying storyline and the explosive wedding crash stunt.
"Emmerdale's groundbreaking live episode and Carl's shocking murder were big hits with the public, as was Corrie's blockbuster wedding that saw Kirsty get her revenge on Tyrone, and EastEnders' massive Christmas Day reveal that Max had a secret wife.
"Awards voted for by the public are the most important ones to the soaps, as it shows what the audience is responding to. There are more drama, tears and explosions than ever in 2013!"
The full winners' list follows below:
Coronation Street: Kirsty falls down the stairs after confronting Tyrone about his affair.
EastEnders: Billy and the Olympic torch
Emmerdale: Emmerdale Live - WINNER!
Home and Away: Rocco dies
EastEnders: Lauren and Joey's car crash
Emmerdale: Katie down the mine
Home and Away: Dex's car crash
Hollyoaks: Wedding day bus crash - WINNER!
Coronation Street: Tina's surrogacy
Coronation Street: Kylie's pregnancy - who's the daddy?
EastEnders: Lola fights for Lexi - WINNER!
Emmerdale: Jai and Rachel's baby secret
Coronation Street: Maria and Marcus
EastEnders: Lauren and Joey
Emmerdale: Cain and Moira
Hollyoaks: Brendan and Ste - WINNER!
Coronation Street: Kirsty and Tyrone - WINNER!
Coronation Street: Nick and Leanne
EastEnders: Christian and Syed
Neighbours: Vanessa and Lucas
EastEnders: Derek is Kat's lover
EastEnders: Kirsty is Max's secret wife - WINNER!
Emmerdale: Chas's stalker uncovered
Hollyoaks: Walker's an undercover cop
Coronation Street: Nick and Leanne's rocky romance
EastEnders: Derek's reign of terror
Emmerdale: Cameron turns killer
Hollyoaks: Esther's bullying - WINNER!
Emmerdale: Carl - WINNER!
Digital Spy Soap Scoop video - press play below to watch Amie Parker-Williams reveal the gossip on Tyrone's Corrie trial, a shock stabbing in EastEnders, danger for Robbie in Emmerdale and Clare's Hollyoaks return.