A control system (12) for an engine (10) having a combustion chamber (22) is disclosed. The control system may have a fuel injector (40) configured to selectively inject fuel into the combustion chamber, and a controller (54) in communication with the fuel injector. The controller may be configured to activate the fuel injector during a first compression stroke to initiate fuel injection in an amount and at a timing that results in a stratified lean air/fuel mixture within the combustion chamber during a first combustion event of a six-stroke cycle. The controller may also be configured to activate the fuel injector during a first power stroke to initiate fuel injection in an amount and at a timing that results in a homogenous lean air/fuel mixture within the combustion chamber during a second combustion event of the same six-stroke cycle.