If you are able to connect to the database from perl, using DBI, you don't need an intermediate file at all.

Use Text::CSV_XS (or Text::CSV) directly to generate the output and it will correctly deal with the quoting:

use strict;
use Text::CSV_XS;

my $csv_in  = Text::CSV_XS->new ({ binary   => 1,   auto_diag => 1,
                                   sep_char => "|", allow_whitespace =
+> 1 });
my $csv_out = Text::CSV_XS->new ({ binary   => 1,   eol => "\n" });
my $infile  = "s.txt";
my $outfile = "s.csv";

open my $fh,  "<", $infile  or die "$infile: $!";
open my $out, ">", $outfile or die "$outfile: $!";
while (my $row = $csv_in->getline ($fh)) {
    $csv_out->print ($out, $row);
    }
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update: corrected $fh to $out in while loop.