Weening, who transferred to Roompot-Oranje Peloton from Australia's Orica-GreenEdge ahead of the 2016 season finished ahead of Etixx-QuickStep's Maximiliano Richeze and Maciej Paterski of the CCC Sprandi Polkowice team.
The general classification witnessed a shake-up in which Kelderman was the strongest of the riders vying for the overall win.
Tejay Van Garderen (BMC), Geraint Thomas (Sky), Rui Costa (Lampre-Merida) and the previous race leader, Pierre Latour (AG2R) all struggled towards the finish of the 162.8km stage from Weese to Amden
Kelderman finished in fifth place, which moved him to the top of the general classification where he’s now leading Warren Barguil (Giant-Alpecin) by 16 seconds. Andrew Talansky (Cannondale Pro Cycling Team) is in third place overall, at 19 seconds.
"It was mainly another cold day,” Kelderman said. "Especially, on the Klaussenpass, it was really cold, foggy and wet. I did not even realise Izagirre was away. Only in the valley, where it was clear, was I warm again.