The following subroutine seems to return the same result as yours, and is about 2 times faster. You didn't provide much testing data, so I'm not sure it will work correctly for the real input.
sub not_so_special { my $s = shift; my @cols = split /;/, $s, -1; my $e; $cols[2] =~ s/=(.+)/'=' . (' ' x length($e = $1))/e; return join ';', @cols, $e }

Update
Or, maybe, more readable and a tiny bit faster:

sub new { my @cols = split /;/, shift, -1; $cols[2] =~ s/=(.+)/=/; $cols[2] .= ' ' x length $1; return join ';', @cols, $1 }

Update 2
This seems even faster (but uglier):

use Syntax::Construct qw{ /r }; sub newer { shift =~ s/^([^;]*;[^;]*;)(.*?=)([^;]*)(;.*)/"$1$2" . (' ' x lengt +h $3) . "$4;$3"/er }
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: split, manipulate, join by choroba
in thread split, manipulate, join by jc.smith3

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