You could keep a counter; and print each item followed by a comma if counter-mod-3, or by a newline otherwise:

@array = qw (1 1 0 2 0 1 3 0 0 4 1 1); 
my $i; 
print $_, ((++$i%3)?",":"\n") for (@array);
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Update:

Per your other question, If (and it may in future) contain references how can i print those and not ARRAY(0x860be48) etc?, ref is your friend:

my $q  = "Q";
my @p  = qw(pee pea);
my %h  = ( one => 1, two => 2, three => 3);
@array = ("1", \@p, "0", "2", "0", \$q, "2", "0", \%h, "4", "1", "1");
my $i;
for my $a (@array) {
   $_ = ref($a);
   print ( /ARRAY/  ? join(':',@$a)      :
           /HASH/   ? join(':',keys %$a) :
           /SCALAR/ ? $$a                :
           $a
         );
   print ((++$i%3) ? "," : "\n" );
}
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