Altermagnetic Josephson junctions (AMJJs) can host unconventional π phase and φ phase despite vanishing net magnetizations. Whether these phases are stable against disorder existing in real materials remains an open question. Here, we investigate impact of disorder on exotic phases in two-dimensional d-wave AMJJs. We show that disorder is able to induce phase transitions between the exotic π and conventional 0 phases, accompanied by a strong suppression of critical current. This behavior is attributed to modifications of the tunneling Cooper-pair phase shift and superconducting decoherence. Remarkably, the anomalous φ phase is highly fragile in presence of disorder and can be driven to either a π phase or 0 phase in a nonreciprocal manner. Across such transitions, the first harmonic of current-phase relation changes sign, while the higher-order harmonics are rapidly suppressed. Our findings reveal the crucial role of disorder in tailoring distinct phases of AMJJs and shed new light on their potential functionalities.