Three people were killed and 12 others were injured when a man opened fire at the Gilroy Garlic Festival in Northern California late Sunday afternoon.

Lynch -- who's the Niners' general manager -- wanted to honor everyone affected by the tragedy ... so he called for 30 seconds of prayer before SF's training camp workout.

"Our community was affected by a horrific tragedy last night down in Gilroy," Lynch said ... "and our players, our team, our organization thought it would be appropriate to start practice with a moment of silence."

Lynch added, "Let's give it 30 seconds to think about the people affected by Gilroy in this community."

As we previously reported ... people began running from the Gilroy festival -- which is just 40 miles from the Niners' stadium -- after gun shots rang out during one of the concerts.

An eye witness, Tommy Huxley, tells TMZ the whole thing was scary as hell ... saying chaos and firework-like sounds filled the festival grounds for minutes.

Law enforcement says the shooter used an AK-47-style rifle ... while witnesses claim he was wearing fatigues and shooting at random.

The father of the 6-year-old who was shot and killed in the gunfire was wearing seen wearing a Jimmy Garoppolo jersey at the hospital shortly after the tragedy.