I wouldn't try to do this using regular expressions but would use a state engine instead.

use strict;
use warnings;

use 5.010;

my $string     =
   q{TestVar(Test1->(xy))->Var2(Test2(10)(12))->Finalvar};
say $string;

my $parenDepth = 0;
my $newString  = q{};

foreach my $char ( split m{}, $string )
{
    if ( $char eq q{(} )
    {
        $parenDepth ++;
    }
    elsif ( $char eq q{)} )
    {
        $parenDepth --;
    }
    else
    {
        $newString .= $char unless $parenDepth;
    }
}

say $newString;
[download]

The output

TestVar(Test1->(xy))->Var2(Test2(10)(12))->Finalvar
TestVar->Var2->Finalvar
[download]

I hope this is helpful.