On the final climb to Roccaraso, Wellens attacked his fellow escapees, soloing 15kms to the summit finish.
But the decisive move came at around 71kms to go when he and Ligthart slipped off the front of the peloton with Laurent Didier (Trek-Segafredo).
They soon bridged the gap to the breakaway and together built up a sizable advantage of 8 minutes and 32 seconds between the climbs with 30kms to race.
Wellens was a little surprised about the gap he was allowed by the peloton.
"But we were all very behind in the GC. I'm glad no team fought behind us. Sometimes you have to be a little bit lucky."
The Belgian was the stage victor but the hero was Ligthart who initiated the decisive move and then worked hard to increase its advantage.
"Ligthart picked the right moment to attack. We felt very very good," Wellens said. "I had a very good feeling and am enormously happy with this victory."
The pace in the bunch barely moved until 24km to go when Orica-GreenEdge and Lampre Merida put in some big efforts. But with a rider of Wellens' calibre ahead a stage win was out of the question.
Vincenzo Nibali's team-mate Jakob Fuglsang (Astana) jumped out of the peloton with 13kms to the summit ultimately finishing second.
With 3kms to go, Tom Dumoulin (Giant-Alpecin) launched his own attack, he and Ilnur Zakarin (Katusha) crossing the line with Fuglsang.
As a result, Dumoulin increased his lead to 26 seconds and the composition of the GC has changed with Fuglsang moving in second overall and Ilnur Zakarin (Katusha) third.
Earlier in the stage, Alexandr Kolobnev (Gazprom-Rusvelo), Alessandro Bisolti (Nippo Vini Fantini) and Eugert Zhupa (Southeast-Venezuela) broke away just after the gun until they were joined by Wellens' group.