Flow separation occurs when adverse pressure gradients (dp/dx > 0) decelerate the boundary layer sufficiently to reverse flow near the wall. The point of incipient separation is marked by zero wall shear stress. Separation creates a wake of recirculating fluid, reducing effective body shape and increasing form drag. The separation point moves upstream at higher Reynolds numbers for bluff bodies and downstream for streamlined shapes.
From your study of boundary layer theory, you know that a thin layer of slower-moving fluid forms near any solid wall, where viscous forces govern behavior. Inside this layer, fluid near the wall has low momentum — it has been slowed by friction. As long as the pressure decreases in the flow direction (a favorable pressure gradient, dp/dx < 0), this low-momentum fluid is still being pushed forward by the higher pressure behind it, and the boundary layer stays attached. The trouble begins when the flow encounters a region of rising pressure.
A pressure gradient is "adverse" when pressure increases in the flow direction (dp/dx > 0). By Bernoulli's equation — your prerequisite — rising pressure means falling velocity. In the freestream, the fluid has enough momentum to decelerate and still keep moving forward. But the near-wall fluid in the boundary layer has already been robbed of momentum by viscous drag. When adverse pressure forces it to decelerate further, it runs out of forward momentum entirely. At the separation point, the wall shear stress τ_w drops to zero: the velocity gradient at the wall is flat. Beyond this point, near-wall fluid actually begins flowing backward — upstream — creating a region of reversed flow beneath the freestream.
Once separation occurs, the boundary layer detaches from the surface and a wake of recirculating, low-energy fluid forms behind the body. Think of a circular cylinder in flow: upstream, the boundary layer attaches nicely; as the flow rounds the curved back half and pressure rises toward the stagnation value, the boundary layer separates near the widest point. The separated wake is a region of low pressure on the leeward side. The upstream face of the cylinder is at high pressure (stagnation), while the separated wake behind it stays at low pressure — this pressure imbalance is the origin of form drag. The body is, in effect, dragging a pocket of low-pressure dead air behind it.
The location of the separation point is not fixed — it depends on the state of the boundary layer. A laminar boundary layer separates earlier (closer to the leading edge) than a turbulent one because turbulent mixing continuously re-energizes the near-wall fluid from the faster outer flow, making it more resistant to reversal. This is the counterintuitive reason golf balls have dimples: the dimples trip the boundary layer turbulent, delaying separation, shrinking the wake, and dramatically reducing form drag. For streamlined airfoils, the gradual pressure recovery along the gently tapering tail keeps dp/dx small enough that the boundary layer stays attached all the way to the trailing edge — at moderate angles of attack. Stall occurs when the angle of attack increases the adverse gradient beyond the boundary layer's ability to resist separation.