Sky star Froome, who has no chance of winning on Sunday, enjoyed a four-second advantage on the stage to Villars-sur-Ollon after a gruelling day negotiating three premier category climbs.
French rider Thibaut Pinot, who was third on the stage right on the wheel of Spain's Ion Izagirre, kept second place overall.
Sunday's fifth and final stage will be over 177.4km from Ollon-sur-Villars to Geneva.