After Nasar is killed, the mayor orders an autopsy, which the village priest must perform since the local doctor is out of town and he had once studied medicine. “It was a massacre,” the narrator reports, and begins to catalogue the wounds made by the Vicario brothers alongside the further damage done by the autopsy, a “second assault.” Nasar’s face becomes unrecognizable, his body, an empty shell which the priest stuffs with rags and quicklime. The stench is overpowering; it engulfs the town.
Essentially, the autopsy's significance stems from the re-brutalization of Nasar. The twins stab him with such vengeance that they are covered with blood themselves, and the main door of Plácida Linero's house, where Santiago was killed, must be repaired by the city. Yet, aside from the Colonel taking their original weapons, the city does nothing to stop the twins' plot. Nasar was initially brutalized (seven wounds were fatal) for a crime that the reader does not really know if he commited, and then he is re-victimized through the carelessness of the priest's autopsy. This maltreatment of Nasar leaves blood on everyone's hands, from the twins themselves to the city as a whole.
And the stench that overpowers the town, representing the "rotten" idea of honor restored. All that happened with the autopsy was an already brutalized body being re-brutalized, and to such a degree that the a proper burial cannot be performed. Nasar, prior to his murder, does not understand why the twins are "hunting" him; as a result, the stench is a reminder of the atrocity perpetrated upon an "innocent" man.