The Rabinowitz-Floer homology of a Liouville domain W is the Floer homology of the Rabinowitz free period Hamiltonian action functional associated to a Hamiltonian whose zero energy level is the boundary of W. This invariant has been introduced by K. Cieliebak and U. Frauenfelder and has already found several applications in symplectic topology and in Hamiltonian dynamics. Together with A. Oancea, the same authors have recently computed the Rabinowitz-Floer homology of the cotangent disk bundle D^*M of a closed Riemannian manifold M, by means of an exact sequence relating the Rabinowitz-Floer homology of D^*M with its symplectic homology and cohomology. The first aim of this paper is to present a chain level construction of this exact sequence. In fact, we show that this sequence is the long homology sequence induced by a short exact sequence of chain complexes, which involves the Morse chain complex and the Morse differential complex of the energy functional for closed geodesics on M. These chain maps are defined by considering spaces of solutions of the Rabinowitz-Floer equation on half-cylinders, with suitable boundary conditions which couple them with the negative gradient flow of the geodesic energy functional. The second aim is to generalize this construction to the case of a fiberwise uniformly convex compact subset W of T^*M whose interior part contains a Lagrangian graph. Equivalently, W is the energy sublevel associated to an arbitrary Tonelli Lagrangian L on TM and to any energy level which is larger than the strict Mane' critical value of $L$. In this case, the energy functional for closed geodesics is replaced by the free period Lagrangian action functional associated to a suitable calibration of L. An important issue in our analysis is to extend the uniform estimates for the solutions of the Rabinowitz-Floer equation - both on cylinders and on half-cylinders - to Hamiltonians which have quadratic growth in the momenta. These uniform estimates are obtained by the Aleksandrov integral version of the maximum principle. In the case of half-cylinders, they are obtained by an Aleksandrov-type maximum principle with Neumann conditions on part of the boundary.