You should really be able to figure out the I/O changes for yourself, but to ensure you follow best practice change:

open my $in1, '<', \$File1;
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to:

open my $in1, '<', $file1 or die "Can't open '$file1': $!\n";
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where $file1 contains the path to input file 1. Do the same for $file2. Add:

open my $out, '>', $fileOut or die "Can't create '$fileOut': $!\n";
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and change the print statement to:

    print $out $line1, ',', (split ',', $line2)[-1];
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(my $line2 = <$in2>) reads a line from $in2 and assigns it to the variable $line2. or last; exits the loop if $in2 contains fewer lines than $in1.