TomDLux's solution totally works, but the below code makes fewer assumptions concerning the nature of the data:

use autodie;
use List::Util qw(max);

use strict;
use warnings;

open my $in1, $file1;
open my $in2, $file2;
open my $out, '>', $file3;

while (! eof($in1) && ! eof($in2)) {
    chomp(my $line1 = <$in1>);
    chomp(my $line2 = <$in2>);
    
    my @line1 = split ' ', $line1;
    my @line2 = split ' ', $line2;

    my @out = map {$line1[$_] - $line2[$_]} (0..max($#line1,$#line2));

    print $out join(' ', @out), "\n";
}

warn "Premature end of file: $file1" if ! eof($in2);
warn "Premature end of file: $file2" if ! eof($in1);
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