The consortium raised its offer in April, for the fourth and final time since October last year, to A$6.20 (£2.59) cents a share.
The number of votes cast in favour of the offer totalled 51.01%, representing 80% of the shareholders, considerably short of the 75% required to get the deal over the line.
Ted Harris, chairman of APN's committee of independent directors, said the bid would have passed if Perpetual had not voted against it.
"If Perpetual had voted in favour of the resolution, it would have passed," he said.
Gavin O'Reilly, IN&M group chief operating officer, said: "Obviously we are cognisant that the majority of shareholders recognise this to be a very good offer.
"I think it is inappropriate at this point to comment on what we may or may not do. I think we want to take stock of the vote."
Had the takeover been successful, IN&M, which currently owns 42% of APN, planned to reduce its stake to 35% and use the proceeds to expand in high-growth markets such as Asia, while Carlyle was due to claim 27.5% and Providence 37.5%.
APN company publishes more than 120 newspapers in Australia and New Zealand, including the New Zealand Herald, and owns several radio stations.
APN shares, which had dropped on expectations the offer would fail, rose 1.2% to A$5.87 at close of business in Australia today.
Independent News & Media publishes 175 newspaper and magazine titles across the globe, including The Independent and The Independent on Sunday.
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