We present composite pulse sequences that perform fault-tolerant two-qubit gate operations on exchange-only quantum-dot spin qubits in various experimentally relevant geometries. We show how to perform dynamically corrected two-qubit gates in exchange-only systems with the leading hyperfine error term canceled. These pulse sequences are constructed to conform to the realistic experimental constraint of strictly non-negative couplings. We establish that our proposed pulse sequences lead to several orders of magnitude improvement in the gate fidelity compared with their uncorrected counterparts. Together with single-qubit dynamically corrected gates, our results enable noise-resistant universal quantum operations with exchange-only qubits.