"This is just getting ridiculous," Waller-Bridge said as she accepted the honour for best comedy series.
"'Fleabag'' started as a one-woman show at Edinburgh Festival in 2013, and the journey has been absolutely mental to get here," added Waller-Bridge, who has also created the show.
"Fleabag'' bested out "Barry", "The Good Place", "The Marvelous Mrs. Maisel", "Russian Doll", "Schitt's Creek" and "Veep" for the honour.
"Season two would not have happened or exploded in the way that it did if it wasn't for Andrew Scott, who came into our 'Fleabag' world like a whirlwind and gave a performance of such depth and complexity that just elevated the whole thing for all of us," she said.
After the win, Waller-Bridge dubbed the wins as a perfect send-off for the show, reports ew.com.
"To be honest, this feels like the most beautiful way to say goodbye to it actually. It does feel like the story is complete. It's so nice to hear that so many people loved it, but it does feel right. We're going out on a high. You can't get higher than this," she added.
Along with the acting category and taking home the big comedy accolade, Waller-Bridge also won an Emmy in the Writing for a Comedy Series category.
"I find writing hard and painful...This is the reason I do it," she said as she showed her Emmy proudly.
"Huge thank you for 'Fleabag' family. Everybody who has put so much heart in it. It's really wonderful to know a dirty, pervy, angry messed-up woman can make it to the Emmys," the actress exclaimed.
"Fleabag" registered another win with Harry Bradbeer taking home the trophy in Directing for a Comedy Series category.
He described the BBC/Amazon show as something that "only comes along once in your life. It was like a perfect storm of support and trust and utter loveliness", and gave a special shout-out to the team, who he said "made something beautiful from almost no money".
The director had a special thank you note for Waller-Bridge.
"Of course, I have to thank Phoebe. Thank you for coming into my life like some kind of glorious grenade. You're extraordinary. You're so trusting. Scientists are still trying to work out how somebody so incredibly talented could be so utterly lovely. This is for you. You're at the centre of it all," he said.
( With inputs from IANS )