Richard Nieuwenhuizen, 41, died on Monday after an under-17 match in Almere on Sunday. He was officiating for the Buitenboys team, for whom his son plays.
Three teenaged players, two aged 15 and one 16, will be charged with manslaughter, assault or public violence over the death of Nieuwenhuizen, according to Dutch prosecutors .
"I would like to express my sadness and distress on hearing of the death of assistant referee Richard Nieuwenhuizen," wrote Blatter in a letter to the Dutch FA (KNVB).
"I was deeply shocked to learn of this tragic incident."
A minute's silence will be held before Thursday's opening match of the Club World Cup between Sanfrecce Hiroshima and Auckland City in Yokohama, FIFA said.
Police arrested the three members of the Nieuw-Sloten Amsterdam youth team after the incident, in which the linesman fell to the ground.
Nieuwenhuizen collapsed hours after the match and was taken to hospital where he fell into a coma. He died the following day.
"Football is a mirror of society and sadly the same ills that afflict society - in this case violence - also manifest themselves in our game," said Blatter.
"Nevertheless, I remain convinced that football - through the example set by the tireless efforts of people like Mr Nieuwenhuizen - is a force for good.
"We must continue to use its positive example to educate people against these wrongs."