This offloads the work to the regex engine and is *much* faster:

sh-3.1$ perl benchmark.pl 
          Rate  split1 substr1   subst
split1  5.05/s      --    -82%   -100%
substr1 27.7/s    449%      --    -99%
subst   3551/s  70273%  12719%      --
ok 1
ok 2
1..2
[download]

The function, could be done in-place which would be even faster:

sub subst
{
    my ($s1, $s2) = @_;

    my $s3 = $s1;

    {
        use bytes;
        $s3 =~ s/(\0)/substr $s2, $+[0]-1, 1/eg;
    }

    $s3;
}
[download]

The complete benchmark file (now with tests):

#!/usr/bin/perl

use 5.6.0;

use strict;
use warnings FATAL => 'all';

use Benchmark qw( cmpthese );
use Test::More 'no_plan';

my $s1 = join '', (do_rand(1) x 100_000);
my $s2 = join '', (do_rand(0) x 100_000);

cmpthese( -2, {
    'split1' => sub { my $s3 = split1( $s1, $s2 ) },
    'substr1' => sub { my $s3 = substr1( $s1, $s2 ) },
    'subst' => sub { my $s3 = subst($s1, $s2) },
});

my $s30 = split1( $s1, $s2 );
my $s31 = substr1( $s1, $s2 );
my $s32 = subst( $s1, $s2 );

is($s30, $s31);
is($s31, $s32);

sub split1 {
  my ($s1, $s2) = @_;

  my @s1 = split //, $s1;
  my @s2 = split //, $s2;

  foreach my $idx ( 0 .. $#s1 ) { 
      if ( $s1[$idx] eq chr(0) ) { 
      $s1[$idx] = $s2[$idx];
  } 
  } 

  return join '', @s1;
}

sub substr1 {
  my ($s1, $s2) = @_;

  for my $idx ( 0 .. length($s1) ) {
      if ( substr($s1,$idx,1) eq chr(0) ) {
      substr($s1, $idx, 1) = substr($s2, $idx, 1);
  }
  } 

  return $s1;
} 

sub subst
{
    my ($s1, $s2) = @_;

    my $s3 = $s1;

    {
        use bytes;
        $s3 =~ s/(\0)/substr $s2, $+[0]-1, 1/eg;
    }

    $s3;
}

# This makes sure that $s1 has chr(0)'s in it and $s2 does not.
sub do_rand {
  my $n = (shift) ? int(rand(255)) : int(rand(254)) + 1;
  return chr( $n );
}
[download]