In practical affine frequency division multiplexing (AFDM) systems, the intricate coupling of oscillator phase noise (PN) and off-grid fractional shifts traps conventional estimators in a severe high-SNR error floor. To address these challenges, we propose a joint PN and channel estimation method based on sparse Bayesian learning (JPNCE-SBL). Specifically, a reduced-rank subspace projection is first introduced to capture the dominant eigen-energy of the Wiener PN process. Concurrently, a dynamic grid evolution strategy is designed to iteratively eliminate off-grid errors without requiring computationally prohibitive global grid densification. Both components are integrated into a unified Expectation-Maximization (EM) framework, where the channel and PN estimates are jointly updated at each iteration to prevent error propagation. Simulation results demonstrate that JPNCE-SBL significantly outperforms existing benchmarks in both NMSE and BER, closely approaching the perfect channel state information case under practical PN conditions.