nohup only does its redirection magic when stdin/stdout/stderr are connected to a tty, that's why you need to explicitly redirect these streams.
Besides that, you can use Net::OpenSSH spawn method to launch the command in the background:
# this code does not check for errors!
my $pid = $ssh->spawn('/usr/sbin/tcpdump -i eth1 -s 1500 -w /tmp/tmp.p
+cap');
($out,$err) = $ssh->capture2('ping -I eth1 -c 3 192.168.107.254');
$ssh->system('killall tcpdump');
waitpid($pid, 0);
($out,$err) = $ssh->capture2('tcpdump -r /tmp/tmp.pcap');
print "THE OUT IS $out\nTHE ERROR IS $err\n";
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