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The female protagonist is in jail, pregnant and confused. She later learns she has been set up by the babies father and loses the baby after suffering both sexual and physical abuse in prison. When she gets out she enacts intricate revenge on everyone involved. I read it in 1999 i believe.

Doesn't match your description 100% but...
If Tomorrow Comes by Sidney Sheldon? Published in 1985.

Tracy is a successful bank-worker in Philadelphia, engaged to a wealthy heir, whose child she is carrying. Then her mother commits suicide, after being scammed by the New Orleans Mafia and left in debt. Tracy gets a gun to frighten the scammer, Joe Romano, into admitting her mother’s innocence, but he tries to rape her and is wounded in the struggle. Her attorney convinces her that she will get a much shorter sentence if she pleads guilty, but the judge sentences her to fifteen years, and she realises that the judge and the attorney are both working for Romano’s boss, mafia don Orsatti. As she goes to jail, her employer and her fiancé abandon her and the unborn child, which she miscarries under the horrendous abuse she suffers from other prisoners.
Tracy now decides to avenge herself on all the men who have ruined her life.

If Tomorrow Comes was what I immediately thought of

That's it! Thank you so much!