Все, придумал:
http {
limit_req_zone $zone_limit_key zone=one:50m rate=2r/s;
limit_conn_zone $zone_limit_key zone=addr:50m;

server {
set $zone_limit_key "${binary_remote_addr}-${host}";
limit_req zone=one burst=5 nodelay;
limit_conn addr 8;
}
}