This is a passive skill and is gained automatically by both the Navy and Pirate Privateer class via the Uncharted Waters expansion pack.
Before starting a fight with a vessel you should click the Sabotage button, this will attempt to sabotage the vessel. Such an action may lower the vessels armor, or hinder its attack potential. The actual effect is entirely random to prevent people from abusing the “strongest” effects. Only one sabotage effect can be in use on a vessel at any one time and they last a number of minutes.
The Sabotage skill does not go up, and will remain at the value it was when you started.