We study the finite temperature transition in QCD with two flavors of dynamical fermions at a pseudoscalar pion mass of about 350 MeV. We use lattices with temporal extent of $N_t$=8, 10 and 12. For the first time in the literature a continuum limit is carried out for several observables with dynamical overlap fermions. These findings are compared with results obtained within the staggered fermion formalism at the same pion masses and extrapolated to the continuum limit. The presented results correspond to fixed topology and its effect is studied in the staggered case. Nice agreement is found between the overlap and staggered results.