As riders began to approach Burgos, Nibali's teammate Diego Ulissi began an early charge away from the pack. But the riders soon bunched up, trying to place themselves tactically for the final sprint.
Paul Voss of Germany, riding for Netapp-Endura, broke away but was shadowed by Mollema, who then burst forward and maintained his sprint to the line.
"The speed dropped a bit and I decided I wanted to attack then and saw there was one guy from the Netapp-Endura team," Mollema said. "So I went behind him and then really kicked off and kept it up to the very end."
On Thursday the riders tackle a grueling 186.5 kilometer (116 mile) mountain stage from Burgos to Pena Cabarga which includes three category 3 climbs, one category 2 peak and a category 1 ascent to the finish.