Your code pushes the entire line onto the array for each match. Is that really what you want? Because that means a line such as the sample you gave causes two elements to be pushed onto the array:

[AlarmForwarderServer.exe,app_common.dll,DsCommon.dll,DSGccCommon.dll,
+DsRffCommon.dll,DsGccProxy.dll,DsRffProxy.dll,]
AlarmForwarderServer.exe,app_common.dll,DsCommon.dll,DSGccCommon.dll,D
+sRffCommon.dll,DsGccProxy.dll,DsRffProxy.dll,
[download]

If your goal is to have a list of dlls associated with each exe, then you should split each line on commas first. The resulting list of strings you can push onto an array:

my @dllarray = map {
        chomp;
        [ split /,/ ]
} @exeDllLines;

# iterate over the collected data:

for ( @dllarray )
{
    my( $exe, @dlls ) = @$_;
    print "$exe uses the following DLLs:\n";
    print "$\t$_\n" for @dlls;
}
[download]

However, a more robust solution would use a hash:

my %exeDll;
for ( @exeDllLines )
{
        chomp;
        my @a = grep /\S/, split /,/; # split on comma; filter out emp
+ty fields
        my @dlls = grep /\.dll$/, @a; # get list of dll files
        for my $exe ( grep /\.exe$/, @a )
        {
                @{$exeDll{$exe}}{@dlls} = ()
                # OR:
                $exeDll{$exe}{$_}++ for @dlls;
        }
}

# then you can iterate over the collected data:

for my $exe ( sort keys %exeDll )
{
    print "$exe uses the following DLLs:\n";
    for my $dll ( sort keys %{ $exeDll{$exe} } )
    {
        print "\t$dll\n";
    }
}
[download]