A control system for a homogeneous charge compression ignition (HCCI) engine includes a timing adjustment module and a combustion control module. The timing adjustment module, per combustion event, advances timings of N fuel injections and retards timings of M fuel injections and spark during a transition from HCCI combustion to mixed-mode combustion. The combustion control module subsequently retards the timings of the N fuel injections and advances the timings of the M fuel injections and the spark to desired timings, respectively, wherein the N fuel injections and the M fuel injections occur sequentially during each combustion event of the HCCI engine, and wherein N and M are integers greater than or equal to zero.