You only have to globally match each sequence of consecutive digits. A global match (in list context) returns all its matches, so this would do

my $line1 = "[HAVE 1324,2,32,324,5,643]";
my $line2 = "[HAVE 4,213,5432,4]";

for ( $line1, $line2 ) {
    my @numbers = /\d+/g;
    print "@numbers\n";
}
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Anno