We study the transition from the Abelian multi-component (3,3,1) quantum Hall state to the non-Abelian one component Pfaffian state in bilayer two dimensional electron systems. We show that tunneling between layers can induce this transition. At the transition points part of the degrees of freedom that describe the (3,3,1) state disappear from the spectrum, and the system is correctly described by the Pfaffian state, with quasi-particles that satisfy non-Abelian statistics. The mechanism described in this work provides for a physical Hamiltonian interpretation of the algebraic projection from the (3,3,1) to the Pfaffian state that has been discussed in the literature.