Your text and example differ slightly. In multiple places the text indicates word 3 comes before words 1 and 2, but your example shows word 3 coming after words 1 and 2. I am assuming you want the latter, but in reality it doesn't impact the choice of data structure.

There are a lot of ways to approach this, but I might use something like

$hash{$word1}{$word2}{$word3} = $count
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where $count is the number of times $word3 is found immediately after (or before) words 1 and 2.

Note that I did not store the percentage, which can be calculated after all of the counts have been accumulated. If you wanted a more complicated structure to facilitate that, you could do something like

$hash{$word1}{$word2}{$word3} =
    { count => $count,
      freq  => $frequency }
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or perhaps even better

$hash{$word1}{$word2} =
    {
        total_counts => $tot_counts,
        words => {
                     $word3 => $count,
                 }
    }
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In the last example you would increment the count for the appropriate $word3 as well as the total_counts for the word pair. This would allow you to easily calculate the frequency for any given $word3 on the fly.^*

To populate the data structure, simply identify words 1, 2, and 3 and then do

$hash{$word1}{$word2}{total_counts}++;
$hash{$word1}{$word2}{words}{$word3}++;
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(or similar, depending on which one you choose).

These structures may be able to be simplified, depending on your requirements. On the other hand, if you had a lot of data and expected the structure to become quite large, a database may be a better choice.

Note that I did not use any arrays. Since the description of the problem implied that you would be looking up data by $word, a hash seemed more appropriate. An array (or an array of hash refs) would require you to search through the contents of the array to find the $word of interest, and depending on the size of the arrays that could be a very inefficient approach.

^*If you really wanted to store the frequency of each word and you didn't need a running total, I'd suggest doing the calculation at the end and using $word3 => { count => $count, freq  => $frequency } rather than $word3 => $count, which would make adding the frequencies later a bit more straightforward.