Green's superb effort looked to have won the game until Scott Wiseman pushed Paul Peschisolido in the 89th minute and Smith tucked away the penalty.
A draw was probably about right for a typical end of season game which only flickered briefly into life, although Hull will claim to have had the better chances.
They certainly came close to scoring a second in the final 10 minutes with Green denied by an agile save from Lee Camp.
The talk before the match centred on Derby's decision to play Miles Addison alongside Lewin Nyatanga in central defence.
It meant they had two 17-year-old centre-backs which is believed to be the youngest pairing in the club's history.
They did little wrong and could not be blamed for Hull's 33rd minute goal which came from nowhere.
A throw-in had been headed out and there looked little danger until Green swung his right foot and the ball fizzed into the top corner of the net.
It was a rare moment of quality in an otherwise drab game although Smith did his best to inspire Derby.
He almost set up a leveller with a low cross that Hull scrambled away and Inigo Idiakez had a 25-yard free-kick which went just over the bar.
But the clearer openings fell to the visitors with Camp just getting his fingertips to another Green drive in the 81st minute and from the resulting corner Kevin Ellison saw his header cleared off the line by Morten Bisgaard.
Ellison was denied by Camp a minute later when he turned and shot from the edge of the box and those saves proved decisive when Derby were awarded a penalty two minutes from time.
Giles Barnes crossed from the right to the back post where Wiseman bundled over Peschisolido and Smith sent Boaz Myhill the wrong way with his spot-kick which nestled into the bottom corner.