An engine control system of a vehicle includes a manifold temperature module, a runner temperature module. The manifold temperature module determines a first temperature of gas in an intake manifold of an engine. The runner temperature module determines a second temperature of gas in an intake runner associated with a cylinder based on the first temperature of the gas in the intake manifold. The engine control system further includes at least one of: a fuel control module that controls fueling of the cylinder based on the second temperature of the gas in the intake runner; and a spark control module that controls spark of the cylinder based on the second temperature of the gas in the intake runner.