Use look-arounds, that way your regex does not consume the next comma.

$ perl -E '
$str = q{1,2,3,,5,6,,,9,10,,,,14,15,,,,,,,,,,,,,};
$str =~ s{(?<=,)(?=,)}{0}g;
say $str;'
1,2,3,0,5,6,0,0,9,10,0,0,0,14,15,0,0,0,0,0,0,0,0,0,0,0,0,
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I hope this is helpful.

Update: If you want the empty last field replaced as well then add an alternation to the look-ahead.

$ perl -E '
$str = q{1,2,3,,5,6,,,9,10,,,,14,15,,,,,,,,,,,,,};
$str =~ s{(?<=,)(?=,|\z)}{0}g;
say $str;'
1,2,3,0,5,6,0,0,9,10,0,0,0,14,15,0,0,0,0,0,0,0,0,0,0,0,0,0
[download]