Tens of thousands of dance music fans from across the globe voted the British three-piece into first place via Mixmag's Facebook page, which hosted a shortlist of 100 dance acts to choose from - although voters were also allowed to add their own nominations.
The end result was incredibly close, with The Prodigy beating French duo Daft Punk by a handful of votes.
Keith Flint, The Prodigy commented: "To walk off a stage and feel like we smashed it - that's the reward for us, to see the crowd react and know we've done what we've come to do. But something like this is truly voted for by the people - and essentially we are nothing without them, so it feels awesome, and really respectful."
Liam Howlett, The Prodigy said: "I'd like to think it's because we kept it real man, because we always do our own thing and try our hardest. Mixmag is the magazine. It's what everyone looks to. It's been around ever since we've been around, too, so it must be doing something right."
Maxim Reality, The Prodigy said: "People like to see a performance that ignites the crowd. We stay true to that and I think they respect it."
Nick DeCosemo, editor of Mixmag commented: "The response to the poll exceeded our wildest expectations and The Prodigy's victory is a wonderful tribute to the passion that they generate in dance music fans everywhere... and the amazing way they have managed to stay just as exciting as ever, over two decades since their first gig.
"The Prodigy have been around almost as long as Mixmag and hopefully we are both still at the top of our respective game."
The Top 20 in full:
1. The Prodigy
2. Daft Punk
3. The Chemical Brothers
8. Fatboy Slim
14. Depeche Mode
16. Basement Jaxx
17. Groove Armada
18. The Shamen
19. Above & Beyond
20. The KLF