In order to brake you need to apply torque in the opposite direction, current needs to flow out of the motor rather than in. The current regulators and svpwm will apply a voltage to the windings to achieve the desired current, in this case a negative iq.
To answer the actual question, when in the off phase of pwm the windings are essentially shorted, allowing the back-emf to produce a current through them. There is now energy stored in the magnetic field. When switching to the on phase, the current still wants to flow, and will produce the voltage necessary to flow back onto the dc bus.
Its kind of analogous to a boost converter, where the windings are the inductor.
