The peloton was whittled down to about a dozen riders on the final category-one climb to La Zubia as Valverde and Nairo Quintana, both of Movistar, took control at the front.
Colombia's Quintana finished fifth behind two former Tour de France champions - Britain's Froome (Team Sky), in second, and Spaniard Contador (Tinkoff-Saxo), in third.
Valverde has a 15-second lead over Quintana in the overall standings, with Contador in third, 18 seconds back, and Froome 22 adrift in fourth.
Ligthart (Lotto Belisol) played a major role in a break for the second day running, taking off with Mas Bonet (Seguros).
They built up a lead of nearly 10 minutes, the biggest of the race so far, and took it up to 14 minutes shortly before leaving the coast near Malaga towards the Sierra Nevada mountains.
Mas Bonet crested the category two Alto de Zafarraya ahead of Ligthart and the two kept the gap at around 10 minutes as the race entered its fourth hour.
The peloton began to reel them in 50 kms from the finish in La Zubia, near Granada, with Katusha and Garmin-Sharp heading the chasing pack, but Ligthart and Mas Bonet were still 4-1/2 minutes ahead with 20 kms to go.
Orica GreenEdge had said they would not try to defend Michael Matthews's overall lead, but the Australian was at the front of the peloton as it entered the last 15 km.
The two riders' lead slipped under one minute as they approached the category one Cumbres Verdes ascent to the finish and Mas Bonet was caught.
Ligthart forged on alone before being joined by Christophe Le Mevel, but both were swallowed up with 3 kms to go as Matthews and Peter Sagan were dropped from a peloton reduced to around 30 riders.
Quintana and Valverde hit the front in the final kilometre at the head of a small group including Froome and Contador, and Valverde surged again in the last 300 metres to win.
(Reporting By Robert Woodward, editing by Pritha Sarkar)
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