The Norwegian, a three-time Grand Slam runner-up, got the better of his British opponent in a two-and-a-half-hour tussle at the Manolo Santana stadium.
Rising star Draper, who will move fifth in the world rankings on Monday above Novak Djokovic, was hoping to add to his Indian Wells title in March, but Ruud outlasted him in his third Masters final.
The 26-year-old, ranked 15th, blinked first with back-to-back double faults to give Draper a break for 2-1 in the first set.
However, in a seventh game hold the Norwegian upped his power and showed his quality, hinting at the fightback which was to follow.
Serving for the set, Draper was unable to polish off his opponent, who broke to tie the set at 5-5.
Ruud held and then broke to claim the first set as Draper mishit a forehand. It was the first set Draper had dropped at the tournament, and he ranted aloud to his team to release his frustration.
His tactic seemed to work as he produced his best tennis in a brilliant second set in which he made just one unforced error and let his rasping forehand shine.
Draper broke in the seventh game for a 4-3 lead, saved two break points in the eighth and then broke again himself to claim the second set, with his third set point.
In the decider, Draper saved three break points to hold in the hard-fought third game, which lasted over 10 minutes.
Ruud broke in the fifth game and consolidated for a 4-2 lead, with his first title of this stature in sight after 12 ATP titles at 250 and 500 level.
The tiring Draper saved a break point in the seventh game despite being docked a first serve for a time violation, and Ruud held for 5-3 to leave Draper serving to stay in the match.
Looking for the first clay court title of his career, the 23-year-old found a second wind and held to love to make Ruud serve it out.
Despite never triumphing at this level, Ruud powered through his final service game, opening up three break points and taking the first, with Draper sending a reply into the stands to end it. (AFP)
