The Santa Clara County District Attorney's Office said the charges stem from a violent attack on his live-in girlfriend at the couple's Los Gatos home on February 11th.
The 49ers made Foster the 31st-overall pick in last year's draft.
"Rueben Foster will not participate in team activities as he is tending to his legal matters", the statement said. "As previously stated, his future with the team will be determined by the information revealed during the legal process".
The decision does not affect felony charges of domestic violence, forcefully attempting to dissuade a witness, and possession of an assault weapon - the latter in connection with a Sig Sauer 516 short-barreled rifle authorities seized from his home.
As a result, it was up to the 49ers as to whether he would participate in any offseason workouts.
"In light of that injunction, this office intends to ask the Santa Clara County Superior Court to dismiss the misdemeanor charge at the next court date scheduled for April 30, 2018", the office said in a statement Monday.
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The 49ers drafted Foster 31st overall previous year after questions about his health and character caused him to drop from being a possible top 10 pick. In a release from the district attorney's office last week, officials said Foster, 24, physically attacked his live-in girlfriend, leaving her bruised and with a ruptured eardrum.
When fullback Bruce Miller was in the midst of legal woes stemming from a domestic incident in 2015, he stayed away from the offseason program; Miller was released prior to the 2016 season after a different arrest for assault.
"The 49ers organization is aware of today's disturbing charges regarding Reuben Foster", the team said in a prepared statement. "We will continue to follow this serious matter", the statement read.
National Football League offseason programs are voluntary and divided into three phases, starting with a two-week session limited to strength and conditioning. Foster's status with San Francisco "will depend on what is learned through the legal process", according to the 49ers (h/t Matt Maiocco of NBC Sports).
"We don't condone this kind of behavior and certainly would not like to see any of our players have any of these kinds of issues or the victims to suffer any at all".