Rapid progress in semiconductor spin qubits has enabled experimental demonstrations of a two-qubit logic gate. Understanding spin decoherence in a two-qubit logic gate is necessary for optimal qubit operation. We study spin decoherence due to 1/f charge noise for two electrons in a double quantum dot used for a two-qubit controlled-phase gate. In contrast to the usual belief, spin decoherence can be dominated by the tunneling noise from 1/f charge noise instead of the detuning noise. Tunneling noise can dominate because the effect of tunneling noise on the spin qubit is first order in the charge admixture; while the effect of the detuning noise is only second order. The different orders of contributions result in different detuning dependence of the decoherence, which provides a way to identify the noise source. We find that decoherence in a recent two-qubit experiment was dominated by the tunneling noise from 1/f charge noise. The results illustrate the importance of considering tunneling noise to design optimal operation of spin qubits.