"Santos FC and Jorge Sampaoli have a signed an agreement for the Argentine to train the team in 2019," the club said in a short statement, adding that some details were yet to be finalised.
The deal marks a return to the dugout for Sampaoli, whose last job was as Argentina coach.
The 58-year-old left the position after a disappointing 2018 World Cup in which Argentina won just one game and were knocked out in the second round.
Sampaoli's biggest coaching achievement was leading Chile to their first ever Copa America title in 2015. He has also worked at clubs in Peru, Ecuador, Chile and Spain, where he coached Sevilla.