High-fidelity quantum gate operations are essential for achieving scalable quantum circuits. In spin qubit quantum computing systems, metallic gates and antennas that are necessary for qubit operation, initialization, and readout, also cause detrimental effects by enhancing fluctuations of electromagnetic fields. Therefore, evanescent wave Johnson noise (EWJN) caused by near-field thermal and vacuum fluctuations becomes an important unmitigated noise, which induces the decoherence of spin qubits and limits the quantum gate operation fidelity. Here, we first develop a macroscopic quantum electrodynamics theory of EWJN to account for the dynamics of two spin qubits interacting with metallic circuitry. Then we propose a numerical technique based on volume integral equations to quantify EWJN strength in the vicinity of nanofabricated metallic gates with arbitrary geometry. We study the limits to two-spin-qubit gate fidelity from EWJN-induced relaxation processes in two experimentally relevant quantum computing platforms: (a) the silicon quantum dot system and (b) nitrogen-vacancy centers in diamond. Finally, we introduce a Lindbladian engineering method to optimize the control pulse sequence design and show its enhanced performance over Hamiltonian engineering in mitigating the influence of thermal and vacuum fluctuations. Our work leverages advances in computational electromagnetics, fluctuational electrodynamics, and open quantum systems to suppress the effects of near-field thermal and vacuum fluctuations and reach the limits of two-spin-qubit gate fidelity.