In internal combustion engines operating in Controlled Auto Ignition (CAI) mode, combustion phasing and heat-release rate is controlled by stratification of fuel, fresh air, and hot internally recirculated exhaust gases. Based on the Representative Interactive Flamelet (RIF) model, a two-dimensional flamelet approach is developed. As independent parameters, firstly the fuel mixture fraction and secondly the mixture fraction of internally recirculated exhaust gases are considered. The flamelet equations are derived from the transport equations for species mass fraction and total enthalpy, employing an asymptotic analysis. A subsequent coordinate transformation leads to the phase space formulation of the two-dimensional flamelet equations. By the use of detailed chemical reaction mechanisms, the effects of dilution, temperature, and chemical species composition due to the internally recirculated exhaust gases are represented. The new approach is tested in phase space, using different variations of operating conditions (i.e., variations of temperature, inhomogeneity, degree of turbulence) typical of CAI engines. Effects of temperature and the composition of the recirculated exhaust gases on combustion, combustion timing, and the location of auto ignition in phase space are individually studied and discussed. The effect of the chemical composition of recirculated exhaust gases is investigated by employing different amounts of oxygen and other chemical species in the internal EGR.