|HP bought Autonomy in 2011 for more than $11bn|
Dutch pension fund manager PGGM led the class action lawsuit, which claimed HP had misled shareholders with the acquisition.
HP said it believed the claim had "no merit" but that it was "desirable and beneficial" to settle the case.
"Further litigation would be burdensome and protracted," it said.
HP paid $11.1bn (£6.8bn) for Autonomy but a year later said it was worth $8.8bn less - sending its shares plunging.
HP's $100m payout will be used to compensate shareholders which bought shares between 19 August 2011 and 20 November 2012, and saw their value fall after the writedown.
Other lawsuits relating to the Autonomy acquisition are still continuing.
Separately HP is pursuing a $5.1bn (£3.6bn) lawsuit against Autonomy, accusing its founder Mike Lynch and ex-chief financial officer Sushovan Hussain of artificially inflating the company's revenue before HP bought the firm.
Both executives have denied the claims.
Source: BBC News