A scheme is proposed for realization of three-qubit Toffoli gate for two intracavity modes with a five-level atom through the atom-cavity resonant interaction in a cavity quantum electrodynamics system. In the presented protocol, the two quantized cavity-field modes act as the two controlling qubits and the two stable ground states of the atom form the target qubit. The numerical simulation shows that the cavity-field decay is the dominant noise source in the dissipative process when both the atomic spontaneous emission and the decay of the cavity modes are taken into account during the gate operation. The influence of the deviation of the coupling strength on fidelity of the three-qubit Toffoli gate and the experimental feasibility of our proposal are also discussed.