Trading space for time (note that delete() on an array is deprecated):

my @sort;
$sort[$_->[2]] = $_ for @masterArray;

my @top = map {delete $sort[-1]} 1..3;

say Dumper \@top;
[download]

Output:

$VAR1 = [
          [
            'this',
            'that',
            300000,
            'something',
            'else'
          ],
          [
            'this',
            'that',
            125638,
            'something',
            'else'
          ],
          [
            'this',
            'that',
            12563,
            'something',
            'else'
          ]
        ];
[download]