Assuming that you really can't use a module (but see Yes, even you can use CPAN), a simple regex substitution does the trick:

use strict;
use warnings;

open my $fh, ">", "tmp.csv" or die "Unable to open $! \n";
#read the file line by line and delimit with commas
print join ",", map {s/(.*,.*)/"$1"/; $_} split /~/ while <DATA>;
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
[download]

Prints:

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
[download]