Stage 18 ran 170km from Melide (Switzerland) to Verbania on Lago Maggiore (Italy), taking the peloton over the little-known category 1 Monte Ologno which defined the day’s events.
Gilbert (BMC) attacked solo out of the remnants of an original 12-man break with less than 20km of racing left to finish ahead of Francesco Bongiorno (Bardiani CSF) and Sylvain Chavanel (IAM).
However the climb on Monte Ologno and later undulating, twisting descent sorted out the contenders from the pretenders with Gilbert, Bongiorno, Chavanel, De La Cruz, Moinard, Siutsou, Busato and Nocentini losing the rest.
As his nearest rival Mikel Landa (Astana) was racing back to the peloton after a mechanical, Contador took the opportunity to extract some time and revenge and attacked with 42km to go and also dropped every other rider in the process.
The remnants of the main peloton, which contained Landa and the rest of the general classification riders, struggled to stay in close proximity to the break and Contador, who was later joined by Cannondale duo Ryder Hesjedal and Davide Villella.
After Gilbert had crossed the finish line the countdown began to see how much time Contador had added to his already considerable lead.
After letting Hesjedal pull ahead as a gesture of goodwill, Contador trailed Gilbert by over six minutes but gained another 1min 12sec on Landa to pad out his already considerable general classification lead to 5min 15sec. Third placed Fabio Aru again struggled and is now 6min 5sec in arrears.
"Today's scenario was a bit different from what happened on the Mortirolo," Contador said. "Before the climb, my team was working hard on the front and expending energy because we knew that we had to be at the front going into the climb, and we wanted to avoid problems.
"Landa was caught behind for the first time in the race so I'm very happy to have gained more time in the general classification. I'm tired, because after the last climb it was a time trial, but every day is hard here."
Stage 18: 170km, Melide (Switzerland) - Verbania on Lago Maggiore (Italy)
1 Philippe Gilbert (BEL) BMC 4hr 4min 14sec
2 Francesco Bongiorno (ITA) Bardiani CSF 0:00:47
3 Sylvain Chavanel (FRA) IAM 0:01:01
4 Matteo Busato (ITA) Southeast
5 Amaël Moinard (FRA) BMC
6 David De La Cruz (ESP) Etixx-QuickStep
7 Rinaldo Nocentini (ITA) AG2R
8 Kanstantsin Siutsou (BLR) Sky
9 Chad Haga (USA) Giant-Alpecin 0:02:42
10 Pieter Weening (NED) Orica-GreenEDGE 0:03:55
1 Alberto Contador (ESP) Tinkoff-Saxo 72hr 23min 9sec
2 Mikel Landa Meana (ESP) Astana 0:05:15
3 Fabio Aru (ITA) Astana 0:06:05
4 Andrey Amador (CRC) Movistar 0:07:01
5 Yury Trofimov (RUS) Katusha 0:09:40
6 Leopold Konig (CZE) Sky 0:10:44
7 Damiano Caruso (ITA) BMC 0:11:05
8 Steven Kruijswijk (NED) LottoNL-Jumbo 0:12:53
9 Ryder Hesjedal (CAN) Cannondale-Garmin 0:13:01
10 Alexandre Geniez (FRA) FDJ 0:14:01