Optical tweezer arrays trapping ultracold atoms and molecules are a versatile quantum science platform with broad impact in quantum simulation, quantum computation, and quantum metrology. The polarization dependence of anisotropic vector and tensor light shifts offers a degree of freedom for precise quantum state engineering of trapped particles. Similarly, state-selective operations depend on the polarization of the addressing light through the atom–light coupling strength. Yet, methods for controlling the polarization of individual tweezers or local addressing beams remain an experimental challenge. Here, we demonstrate independent, site-resolved linear polarization rotation across an optical tweezer array by exploiting the local birefringence tunability of a spatial light modulator. Applying this capability to an array of ⁸⁸rmSr atoms, we homogenize differential light shifts imparted by the 813-nm tweezers to the narrow ¹rm S₀↔³rm P₁ transition, enabling sideband cooling under a magic-angle condition. Furthermore, we show dynamic transport of trapped atoms across distinct polarization zones with high survival and preserved coherence. Finally, we characterize tweezer polarization noise and demonstrate closed-loop stabilization referenced to the atomic transition frequency, reaching mrad-level stability. Our work establishes a technique for manipulating polarization-sensitive atomic and molecular transitions in tweezer architectures, with immediate applications to optical tweezer clocks and multi-zone quantum processors.