Two months to the day that he broke his leg on stage 10 of the Tour de France the Tinkoff-Saxo team leader avoided any late drama to secure the red jersey for the second time in three years.
Beginning the final day of the 21-stage race the Spaniard held a one-minute-37-second lead over Team Sky's Chris Froome and negotiated the 9.7-kilometre time trial for the loss of only 27secs.
Contador's victory sees him pull alongside Roberto Heras and Tony Rominger as only the third rider to have claimed three wins in the Grand Tour.
Froome secured his second place behind Contador with the 63rd-fastest ride of the time trial, while Alejandro Valverde took the final podium place for Movistar a further 40secs back.
Meanwhile, Luis Leon Sanchez (Caja Rural) took the king of the mountains jersey and John Degenkolb (Giant-Shimano) earned himself the sprinters' green jersey.
With rain affecting the course the timings were not as quick as many expected and Malori's effort of 11mins 12 secs remained the mark to beat all the way until Contador left the start ramp over three hours later.
Malori (Movistar) was the 44th rider to take to the circuit around Santiago de Compostela but nobody was able to get near him, with Jesse Sergent (Trek Factory Racing) eight seconds back in second place.
The leaders experienced better conditions later in the day but were unable to use it to their advantage as Malori's time remained out of reach.
As well as sharp bends and fast downhill segments the riders had to negotiate tricky cobbled sections before finishing on the winding streets next to Santiago's cathedral.
The final five runs saw Fabio Aru (Astana), Joaquim Rodriguez (Katusha), Valverde and Froome look to set the fastest time but the conditions meant Malori earned the win and Contador the title.