Richard French, a barrister specialising in such cases, said he believed it was the first time the MoD has ever apologised in this way.
The out-of-court settlement comes just two weeks after a former Wren, Lesley Morris, won pounds 65,000 compensation in a similar case.
The MoD said there were hundreds of cases of this kind and could not confirm it was the first time such an apology had been issued, but the case does set a precedent for many more out-of-court settlements.
Alisa Cook, a former lieutenant, was awarded an "undisclosed sum". Neither she nor Mr French would say how much, but it is understood to be several thousand pounds. The industrial tribunal was due to start at Southampton on Monday but was halted yesterday.
Lt Cook left the Army in 1995 after claiming she had been subjected to a terrifying campaign of bullying and harassment by male junior officers while serving with the Royal Artillery.
In the most dangerous and frightening incident, a CS riot-control gas grenade was hurled into her shower room.
The MoD accepted that such treatment may have had an adverse effect on Ms Cook's self-confidence and will to continue with her Army career.
Ms Cook had joined the Army in 1984 and served in the ranks for about eight years before being selected for a commission and training at Sandhurst. Her ill-treatment began when she arrived at her unit in 1992.
"Since I left there have been so many changes", she said. "I am aware from my friends who are still serving that they are stamping out initiation ceremonies and bringing in equal opportunities training."
The 33-year-old former officer said last night the apology was a sign of important change in the armed forces.
"I never thought I would get it", she said. "When Richard [French] called and told me just knocked me for six. It says a lot for them [the Army].
"They have accepted there was unacceptable treatment levelled at me. They have accepted what happened and are willing to say sorry."
Ms Cook said she had never thought in terms of a financial settlement, but only to receive an apology.
"Money was not the issue and it never was," she said last night.
Mr French, who specialises in employment law and took Ms Cook's case free of charge, added: "For a lot of women all they want is for someone to recognise that something happened which should not have happened.
"The mere fact that the MoD was prepared to apologise in public for something that occurred five years ago is in itself significant."
Ms Cook said she was now looking forward to her future and possibly returning to university.Reuse content