San Francisco 49ers owner Jed York pulled the plug on his marriage three months before he was arrested on suspicion of engaging in prostitution ... TMZ Sports has confirmed.

Jed beelined it to Santa Clara Superior Court back in May and filed to divorce his wife, Danielle York, after more than 15 years of marriage ... according to legal docs obtained by TMZ Sports.

In his filing, Jed went with the boilerplate "irreconcilable differences" as the reason for the split.

The docs show Jed and Danielle agreed to joint legal and physical custody of their two children, ages 13 and 10. The estranged couple is still determining how to divvy up assets and property. It's unclear if there's a prenup.

As we reported ... Jed was arrested Sunday in East Palestine, Ohio, after allegedly arranging to pay $140 for sex at a trailer park. He cut a plea deal and pled no contest to a pair of misdemeanor charges -- one count of disorderly conduct and one count of possessing criminal tools.

It looks like the "criminal tool" is his cellular phone, which Jed allegedly used to reply to an ad posted on a prostitution website and set up a meeting.

Jed is from Ohio ... and he was arrested near his family's home.