Holder is the only player to miss out from the ODI side that lost to India 2-1 recently.
Windies will take on Ireland in three ODIs - the first two to be played at Kensington Oval, Barbados while the last will be played at the National Cricket Stadium in Grenada. The two sides will then contest in three T20Is scheduled for a later date.
"The decision was taken to rest Jason due to the heavy workload he has had over the last year," International Cricket Council (ICC) quoted West Indies' selector Roger Harper as saying.
"With an important year ahead for West Indies cricket, we saw this as the best opportunity to give him a break to recharge his batteries and refresh his mind so he could be ready to perform at his best as our Test captain throughout 2020, as the number one ranked all-rounder in Test cricket and an important member of the team in the white-ball formats", the statement read.
"This series against Ireland offers us the opportunity to build on the performances in India, build confidence as a team and for individual players. Just like the series against Afghanistan, the Ireland series is an important one for us, one we must win," Harper added.
Squad: Kieron Pollard (c), Sunil Ambris, Roston Chase, Sheldon Cottrell, Shimron Hetmyer, Shai Hope, Alzarri Joseph, Brandon King, Evin Lewis, Keemo Paul, Khary Pierre, Nicholas Pooran, Romario Shepherd, Hayden Walsh Jr.
The first ODI between Windies and Ireland will be played in Barbados on January 7.