Just for the alternative, splitting on TAB triggers me to mention Text::CSV_XS (using toolic's hash approach):

use strict;
use warnings;
use Text::CSV_XS;

my $csv = Text::CSV_XS->new ({ sep_char => "\t", auto_diag => 1 });
my %Diag;
while (my $row = $csv->getline (*DATA)) {
    push @{$Diag{$row->[0]}}, $row->[1];
    }

$csv->eol ("\n");
$csv->sep_char (",");
$csv->print (*STDOUT, [ $_, @{$Diag{$_}} ]) for sort keys %Diag;

__DATA__
Name1   1234
Name2   9999
Name1   5514
Name3   5415
Name2   6419
[download]

-->

Name1,1234,5514
Name2,9999,6419
Name3,5415
[download]