Valverde led much of mountainous Stage 17 and built a large lead that he was able to keep for the stage victory.
However, finishing second was Chris Froome with his Sky Procycling teammate Wiggins in third. That allowed Wiggins to increase his overall lead on everyone in the field except Valverde, who is well back in the overall classification, and Froome.
Valverde pulled away from the lead group about 65 miles into the race and had a good lead by the time he reached the final Category 1 climb that marked the end of Thursday's ride. Even then, Wiggins and Froome steadily cut into the lead before settling for a 2-3 finish.
Valverde covered the 89.1-mile route from Bagneres-de-Luchon to the Peyragudes ski resort in 4 hours, 12 minutes, 11 seconds. Froome and Wiggins were closing in the final mile or so of the race and ended up 19 seconds back.
While Wiggins stays 2 minutes, 5 seconds ahead of Froome, who is second overall, he increased his edge on third-place Vincenzo Nibali to 2:41 with three stages to go.
Jurgen Van Den Broeck, who is 5:53 back, is the only other rider within 8 minutes of the lead.
Friday's Stage 18 is a 138.3-mile run across southern France north from Bagnac-sur-Cele to Brive-La-Gaillarde.