Try the index function for finding the zero bytes in $s1.

(udpate: fixed typo)

Another update: now with complete code: 

sub windex {
    my ($s1, $s2) = @_;
    my $pos = -1;
    my $null = chr 0;
    my $len = length $s1;
    while( ($pos = index $s1, $null, $pos+1) >= 0 ){
        substr $s1, $pos, 1, substr($s2, $pos, 1);
    }
    return $s1;
}

[download]

It's fast, but it won't win the beer: 

          Rate  split1 substr1   index
split1  4.32/s      --    -84%   -100%
substr1 27.7/s    541%      --    -99%
index   3757/s  86900%  13478%      --

[download]

But don't bother, I don't like beer.. ;-)

Another update: fixed initial value of $pos. See Re: Challenge: CPU-optimized byte-wise or-equals (for a meter of beer) and the follow ups for more details.

In reply to Re: Challenge: CPU-optimized byte-wise or-equals (for a meter of beer) by moritz
in thread Challenge: CPU-optimized byte-wise or-equals (for a meter of beer) by dragonchild

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