Photovoltaic manufacturing is material intensive with the cost of crystalline silicon wafer, used as the substrate, representing 40% to 60% of the solar cell cost. Consequently, there is a growing trend to reduce the silicon wafer thickness leading to new technical challenges related to manufacturing. Specifically, wafer breakage during handling and/or transfer is a significant issue. Therefore improved methods for breakage-free handling are needed to address this problem. An important pre-requisite for realizing such methods is the need for fundamental understanding of the effect of handling device variables on the deformation, stresses, and fracture of crystalline silicon wafers. This knowledge is lacking for wafer handling devices including the Bernoulli gripper, which is an air flow nozzle based device. A computational fluid dynamics model of the air flow generated by a Bernoulli gripper has been developed. This model predicts the air flow, pressure distribution and lifting force generated by the gripper. For thin silicon wafers, the fluid model is combined with a finite element model to analyze the effects of wafer flexibility on the equilibrium pressure distribution, lifting force and handling stresses. The effect of wafer flexibility on the air pressure distribution is found to be increasingly significant at higher air flow rates. The model yields considerable insight into the relative effects of air flow induced vacuum and the direct impingement of air on the wafer on the air pressure distribution, lifting force, and handling stress. The latter effect is found to be especially significant when the wafer deformation is large. In addition to silicon wafers, the model can also be used to determine the lifting force and handling stress produced in other flexible materials. Finally, a systematic approach for the analysis of the total stress state (handling plus residual stresses) produced in crystalline silicon wafers and its impact on wafer breakage during handling is presented. Results confirm the capability of the approach to predict wafer breakage during handling given the crack size, location and fracture toughness. This methodology is general and can be applied to other thin wafer handling devices besides the Bernoulli gripper.