In this work, a direct mixed quantum-classical dynamics approach is presented, which combines two new computational methodologies. The nuclear dynamics is solved by the decoherence-induced surface hopping based on the exact factorization (DISH-XF) method, which is derived from the exact factorization of the electronic-nuclear wave function and correctly describes quantum decoherence phenomena. The state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS, or SSR, for brevity) electronic structure method is based on ensemble density functional theory (eDFT) and provides correct description of real crossings between the ground and excited Born-Oppenheimer electronic states. The new combined approach has been applied to the excited-state nonadiabatic dynamics of the trans-penta-2,4-dieniminium cation (PSB3). The predicted S1 lifetime of trans-PSB3, τ = 99 ± 51 fs, and the quantum yield of the cis conformation, ϕ = 0.63, agree with the results obtained previously in nonadiabatic molecular dynamics simulations performed with a variety of electronic structure methods and dynamics formalisms. Normal-mode analysis of the obtained classical nuclear trajectories suggests that only a few vibrational normal modes contribute to the nuclear wavepacket; where synchronization between several modes plays a dominant role for the outcome of photoisomerization.