The three riders who cross the line first will be awarded 20, 12 and eight seconds respectively.
In the 2012 edition these bonuses were eliminated on the five mountain stages but remained in place for the flat stages.
They are never awarded in time trials.
The 96th Giro will also see the addition of a second intermediate sprint on each stage, with five, three and two seconds awarded for the first three riders to cross the line.
In 2012 the solitary sprint bonus on each stage saw six, four and two seconds awarded.
The race will start on May 4 in Naples and conclude on May 26 in Brescia.
In 2008 the Tour de France scrapped all time bonuses as they can have a large impact on the General Classification.
In the 2011 Vuelta a Espana Chris Froome lost the overall title by 13 seconds to Juan José Cobo - but without the 32 seconds the Spaniard won in bonuses, the Briton would have won by 19 seconds.