A variety of methods and arrangements are described for selectively reducing intake manifold pressure in a skip fire engine control system. In some embodiments, a throttle is adjusted to generate a manifold vacuum, which is used for various applications, including but not limited to purging a fuel vapor canister, reducing pressure within a brake vacuum booster reservoir and/or venting gas from a crankcase interior. An engine firing fraction is increased to help maintain a desired torque level. Other techniques for reducing the intake manifold pressure are also described, such as applications involving a return to idle.