Spain's Contador, who had not won a stage race since the 2012 Tour of Spain on his return from a doping ban, outwitted his rivals to claim two consecutive stage victories on Saturday and Sunday.
Movistar rider Adriano Malori won Tuesday's final individual time trial ahead of Swiss Fabian Cancellara and Britain's Bradley Wiggins, but Contador kept the blue jersey after finishing 29th in the 9.1-km effort against the clock.
Second overall 2:05 off the pace was Colombian Nairo Quintana, who was no match for Contador during Sunday's stage which featured a gruelling uphill climb.
Conatdor's Tinkoff-Saxo team mate Roman Kreuziger of the Czech Republic took third place, nine seconds further back.
Briton Froome, who had no rival on last year's Tour and finished the three-week race over six minutes ahead of fourth-placed Contador, sat out of Tirreo-Adriatico because of back pains.
Both riders, however, will start the Tour of Catalunya next week, three and a half months before the Tour de France's Grand Depart in Leeds.
Stage seven results
1. Adriano Malori (Italy / Movistar) 10:13"
2. Fabian Cancellara (Switzerland / Trek) +6"
3. Bradley Wiggins (Britain / Team Sky) +11"
4. Tony Martin (Germany / Omega Pharma - Quick-Step) +15"
5. Tom Dumoulin (Netherlands / Giant) +19"
6. Alex Dowsett (Britain / Movistar) +20"
7. Michal Kwiatkowski (Poland / Omega Pharma - Quick-Step) +22"
8. Manuel Quinziato (Italy / BMC Racing) +23"
9. Stijn Devolder (Belgium / Trek) +24"
10. Luke Durbridge (Australia / Orica) +26"
1. Alberto Contador (Spain / Tinkoff - Saxo) 25:28:45"
2. Nairo Quintana (Colombia / Movistar) +2:05"
3. Roman Kreuziger (Czech Republic / Tinkoff - Saxo) +2:14"
4. Jean-Christophe Peraud (France / AG2R) +2:39"
5. Julian Arredondo (Colombia / Trek) +2:54"
6. Domenico Pozzovivo (Italy / AG2R) +3:04"
7. Robert Kiserlovski (Croatia / Trek) +3:09"
8. Daniel Moreno (Spain / Katusha) +3:16"
9. Michele Scarponi (Italy / Astana)
10. Mikel Nieve (Spain / Team Sky) +3:19"
- Sports & Recreation
- Bradley Wiggins
- Fabian Cancellara
- Adriano Malori
- Nairo Quintana
- Roman Kreuziger