You should probably be using a hash instead.

my %hash;
while (my ($filename, $number) = &get_both) {
   $hash{$filename} = $number;
}

my @sorted_files = sort { $hash{$a} <=> $hash{$b} } keys %hash;
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If you really need to put this in an array (to keep track of the insertion order, for example), you could probably do it like this:

my @array;
while (my ($filename, $number) = &get_both) {
   push(@array, [ $filename, $number ]);
}

my @sorted = sort { $a->[1] <=> $b->[1] } @array;
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