#!/usr/bin/perl
use warnings;
use strict;

use Text::CSV;
my $csv = Text::CSV->new;
open my $FH, '<', '1.csv' or die $!;
while (my $row = $csv->getline($FH)) {
    s/,/~/g for @$row;
    $csv->combine(@$row);
    print $csv->string, "\n";
}
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use strict;
use warnings ;


my @csv = <DATA>;

foreach my $line ( @csv ) { 
    my $clean_line = $line ;
    while( $line =~ /"(.*?)"/g ) { 
    my $match = $1 ;
    my $match_cleaned = $match ;
    $match_cleaned =~ s/,/~/g;
    my $location = index( $line, $match ) ;
    my $clean_line = substr( $clean_line, $location, length( $match ),
+ $match_cleaned );
    }
    print "$clean_line";
}

__DATA__
123,abc1,test1,"1,3,5",new,"abc,dfg,hj"
124,abc2,test2,"1,3,5",new,"abc,dfg,hj"
125,abc3*,test3,"*|1,3,5",new,"abc,dfg,hj"
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Notice that replace withing $line is not done using a regex - this is to avoid escaping $match and to also speed things up.

You can compress this code but its been stretched out for readability.

Yes, and pray for \" not appearing in the data.
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

Thanks for help and input. below code works fine:

my $file = "t.txt";
open(FH,$file) || die "can't open file \n";
while (<FH>) {
    chomp;
    my $line = $_;
    $line =~ s/\"(.*?)\"/replace($1)/ge;
    $line =~ s/\,/~/g;
    $line =~ s/\;/,/g;
    print "$line \n";
}
close FH;
sub replace {
    my ($str) = @_;
    $str =~ s/\,/\;/g;
    return $str;
}
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