Froome was over three minutes behind the winner on the mountainous 160km stage from Bourg-en-Bresse to Culoz, but finished alongside his main rivals.
Colombian Pantano (IAM Cycling) outsprinted Poland's Rafal Majka to claim his maiden Grand Tour stage win.
Dutchman Bauke Mollema and Briton Adam Yates finished in the peloton to stay second and third overall.
Movistar's Nairo Quintana, fourth in the general classification and two minutes 29 seconds behind Froome, is the man most likely to make a move for the yellow jersey, but he showed few signs of attacking in the Jura Mountains.
