The list is a countdown of the year's most popular songs voted for by listeners of the alternative music station.
Triple J said there were "a whole range of reasons" behind the decision.
The main one is a social media campaign, originally instigated by Buzzfeed Australia's Mark Di Stefano, to get Shake It Off on the list.
Readers were encouraged to tweet #Tay4Hottest100 to get the song to appear on the countdown, which was thought to be too much of an influence.
Some thought Swift's track was too commercial for the alternative music station, while others said banning the song would be seen as elitism.
The list was topped by Chet Faker's Talk Is Cheap, with Peking Duk's High and Cosby Sweater by Hilltop Hoods completing the top three.
Mark Ronson's Uptown Funk finished sixth on the poll, while alt-J have three songs in the top 30.
Triple J pointed out that Taylor Swift wasn't played at all on the station in 2014 but would have finished ahead of all alt-J's tracks if it wasn't disqualified.
Vance Joy's Riptide won the 2013 poll, which saw a more commercial top three include Lorde's Royals and Get Lucky by Daft Punk.
Triple J presenter Lewis McKirdy, who made the announcement that Taylor Swift's track wouldn't be allowed in the list, directed listeners to a Buzzfeed parody titled 8 Hilarious But Totally True Reasons You Didn't Hear Shake It Off In The Hottest 100, for more information about the decision.
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Simeone, 44, has led Atletico to a host of trophies since becoming coach in 2011, including last season's La Liga title and the 2012 Europa League crown.
They were runners-up to Real Madrid in the 2014 Champions League final, who they face in this season's last eight.
"I am here because I'm convinced the club will continue to grow," he said.
Simeone is widely regarded as one of the best coaches in European football, and was reported to have been linked with a number of clubs, including Manchester City.
"Nobody embodies the values of our club more so than Simeone," said club president Enrique Cerezo.
The Argentine guided Atletico to their first title since 1996 last year with a last-day draw at Barcelona.
His side were then seconds away from winning the Champions League until Sergio Ramos's header took rivals Real into extra-time.

The company's flotation on the Nasdaq stock exchange had initially raised a less-than-expected $286m (Â£170m).
However, investors flocked to the shares, and they ended the day at $20.24, after opening at $17.
The number of Weibo users fell after China's censors strengthened control of online discussions last year.
The China Internet Network Information Center said in its annual report that almost 28 million people abandoned Weibo in 2013.
The sale is a big test of demand for Chinese internet stocks ahead of an anticipated listing by Weibo's co-owner, the Alibaba group.
China's internet market has grown to become the world's biggest with more than 500 million users.
With major global social networking firms such as Facebook and Twitter blocked in the country, domestic companies have benefited the most from this growth.
However, the growing popularity of social media platforms has also attracted the attention of authorities who have moved swiftly to silence voices online.
Triple J have confirmed Taylor Swift was disqualified from this year's Hottest 100.
[NEXT_CONCEPT]
Coach Diego Simeone has signed a contract extension with Atletico Madrid that will keep him at the Spanish champions until 2020.
[NEXT_CONCEPT]
Shares in China's Weibo, a Twitter-like service, rose by almost 20% on their first day of trading on the US stock market, after a lukewarm start.