Lean operation of Spark-Ignition engines can provide higher thermal efficiency compared to standard stoichiometric operation. However, for a homogeneous lean mixture, the associated reduction of flame speeds becomes an important issue from the perspective of robust ignition and fast flame spread throughout the charge. This study is focused on the use of a lean partial fuel stratification strategy that can stabilize the deflagration, while sufficiently fast combustion is ensured via the use of end-gas autoignition. The engine has a spray-guided Direct-Injection Spark-Ignition combustion system and was fueled with either a high-octane certification gasoline or E85. Partial fuel stratification was achieved using several fuel injections during the intake stroke in combination with a small pilot-injection concurrent with the Spark-Ignition. The results reveal that partial fuel stratification enables very stable combustion, offering higher thermal efficiency for parts of the load range in comparison to well-mixed lean and stoichiometric combustion. The heat release and flame imaging demonstrate that the combustion often has three distinct stages. The combustion of the pilot-injected fuel, ignited by the normal spark, acts as a “super igniter,” ensuring a very repeatable initiation of combustion, and flame incandescence reveals locally rich conditions. The second stage is mainly composed of blue flame propagation in a well-mixed lean mixture. The third stage is the compression autoignition of a well-mixed and typically very lean end-gas. The end-gas autoignition is critical for achieving high combustion efficiency, high thermal efficiency, and stable combustion. Partial fuel stratification enables very effective combustion-phasing control, which is critical for controlling the occurrence and intensity of end-gas autoignition. Comparing the gasoline and E85 fuels, it is noted that achieving end-gas autoignition for the higher octane E85 requires a more aggressive compression of the end-gas via the use of a more advanced combustion phasing or higher intake-air temperature.