A control system for a dual-fuel engine is disclosed. The control system may have a gaseous fuel injector having a nozzle located at a first air intake port of a cylinder of the engine and configured to inject a variable amount of gaseous fuel radially into the cylinder based on at least one of a load and speed of the engine. The control system may also have a liquid fuel injector configured to inject a fixed amount of liquid fuel axially into the cylinder based on the at least one of the load and speed of the engine. The control system may additionally have a regulator configured to selectively adjust a flow of gaseous fuel to the gaseous fuel injector and at least one sensor configured to generate a signal indicative of a performance parameter of the engine. The control system may also have a controller in communication with the regulator and the at least one sensor. The controller may be configured to selectively cause the regulator to adjust the flow of gaseous fuel based on the signal.