It was the Scot's fourth win here (he scored a hat-trick from 1983 to 1985) as well as his first three-day event victory since he became European champion at Punchestown in 1991.
Stark won from the overnight leader, Pierre De Bastard of France on Tresor du Cochet, who dropped back to second after three show jumping errors.
Leslie Law moved up one place to finish third on Cruiseway, a handsome eight-year-old who was bred by his owner, Alan Spiers.
Stark and Law seem certain to be named for the British Olympic squad today with their Badminton mounts, Stanwick Ghost and New Flavour. William Fox-Pitt also looks assured of one of the seven places after jumping clear cross-country and show jumping rounds here on Cosmopolitan II, who was running hors concours and was not eligible for any prizes.
Mary King, who was on a similar mission with Star Appeal, has abandoned any idea of taking the horse to the Olympics after a fall at the 17th cross-country fence. She is, however, sure to be chosen with King William.
Lucy Kemplay, 19, rode Heron's Flight to win the Yorkshire Post Young Riders National Championship for the second year running.