The unit was reconnected to the grid at 1108 local time (0808 GMT) and its operating normally, the power plant said in a statement.
An element from the management system of the unit's generator failed on Tuesday, activating the automatic shutdown. The incident occurred in the non-nuclear part of the unit.
Unit Six was switched off on September 15 for routine annual maintenance and came back on stream on Saturday at 1415 local time.
The plant also said that it will start to gradually power down Unit Five before switching it off for a week's maintenance ahead of the winter season.
Kozloduy remained with just two 1,000 MW operational reactors after the government closed down four units of 440 MW each to address nuclear safety concerns of the European Union prior to the country's accession to the bloc. Bulgaria joined the EU in 2007.