Here is the simple regex logic without spliting the input

#! /usr/bin/perl

use strict;
use warnings;

open my $fh,">","tmp.csv" or die "Unable to open $! \n";
while(<DATA>){
        $_ =~ s/(\S+,)+([^~]*)/"$1$2"/g if $_ =~ /,/;
        $_ =~ s/~/,/g;
        print $fh "$_";
}
close $fh;

__DATA__
col1~col2~col3~col4~col5
data11~data12~data13~data14~data15
data21~data22~data23~data24~data25
data31~data32~data33~data34~data35
data,data41~data42~data43~data44~data45
data51,data52,data,junk,specialchar,sometingdata53~data54~data55
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