use strict;
use warnings;

my ($user, $third, @data);

$user = 'Thomas';
$third = 'newvalue';

chomp(@data = <DATA>);
for (@data) {
    # Skip if user is not $user
    next if !m/^\Q$user\E\s*:/;
    # Change third field and exit loop
    @_ = split /:/, $_;
    $_[2] = $third;
    $_ = join ':', @_;
    last;
}

# Print data back to file (replace this)
print $_, "\n" for @data;

__DATA__
Username   :  Password  :   Download |
Tom       :   12345678  :
Thomas     :  12345678   :  121312313123131313
[download]