Yates, a former track racer whose road racing talents took him to the brink of victory in this year's Giro d'Italia, all but wrapped up overall victory on Saturday after another strong finish on the final mountain stage.
After a largely processional final stage to Madrid on Sunday claimed by Elia Viviani, the 26-year-old Englishman – riding for the Mitchelton team – crossed the line after the 3,271.4 kilometre race in an overall time of 82 hours, five minutes and 58 seconds.
Enric Mas from Spain finished second overall and the Colombian Miguel Angel Lopez was third.
It was Yates's first victory in a three week race and comes months after the disappointment of losing May’s Giro d'Italia, having controlled the race for much of the opening two weeks.
On that occasion, Team Sky’s Chris Froome capitalised on Yates's collapse in the mountains to secure the race's pink jersey and seal his third consecutive Grand Tour after winning the Tour de France and Tour of Spain in 2017.
Froome's winning streak came to an end in July, when teammate Geraint Thomas, who also honed his skills on the track, upset the Kenyan-born Briton to triumph at the Tour de France.
Yates's triumph on Sunday means British riders have dominated all three Grand Tours in 2018.