The Court of Appeal ruled that Mrs Ilott would otherwise face a life of poverty because she was on benefits and could not afford to go on holiday or buy clothes for her children.
The fact that Mrs Jackson had little connection to the charities to which she left her money played a part in the ruling, the judges said.
Legal experts said the ruling had implications for how people needed to draw up their wills. They said it suggested that people would in future have to explain their reasons for why they had left money to certain parties and demonstrate tangible connections to them.
It will also make it easier for adult children who are disinherited by their parents to challenge their wills and gain a proportion of any estate, according to lawyers.
Gary Rycroft, a member of the Law Society's wills and equity committee, said: "This ruling is saying that while you can still disinherit your children, you are going to have to explain why and show connections with those you are leaving the money to.
"It is also very important because it seems to be making it easier for adult children to claim for reasonable financial provision in wills and has made the gap wider for them to do that."
James Aspden, the solicitor who represented the three animal charities, the RSPB, the RSPCA and Blue Cross, said: "This is a worrying decision for anyone who values having the freedom to choose who will receive their property when they die."
Mrs Jackson was described in court as "unreasonable, capricious and harsh" and had "unreasonably excluded" her daughter from her will.
Mrs Jackson's relationship with her daughter broke down when she ran off with her future husband, Nicholas Ilott, when she was 17. The couple went on to have five children, three of whom are now over 18. Failed attempts at a reconciliation were blamed on both sides.
Mrs Ilott's father died before she was born and the final falling out came when she named her fifth child after her paternal grandmother, whom her mother did not like, the court heard, Before her death in 2004, Mrs Jackson wrote in a letter to lawyers: "I can see no reason why my daughter should benefit in any way from my estate.
"I have made it clear to my daughter ... that she can expect no inheritance from me when I die."
The widow explicitly instructed the executors of her will to fight any claim Mrs Ilott might make after her death.
Mrs Ilott challenged the will in 2007 under a right to "reasonable provision" which is contained in the 1975 Inheritance Act. It is normally used for young children who are left out of wills, but in 2011, Mrs Ilott won £50,000 from the estate before challenging for more money. She lost in the High Court last year but succeeded in the Court of Appeal.
Lady Justice Arden awarded her £164,000 to allow her to buy her housing association home in Ware, Herts, with £20,000 left over to supplement her benefits. The judges drafted the ruling so that she would not lose her state benefits.
However, one of the three judges, Sir Colin Rimer, said the award should be limited and that it was "reasonable" for her to attempt to find work over the next few years. Mrs Ilott's barrister, Brie Stevens-Hoare QC, said the family were living on the breadline.
Mr Apsden said the charities would give "very careful consideration" to the case before deciding whether or not to appeal to the Supreme Court.
Sally de la Bedoyere, chief executive of Blue Cross, said: "We have defended the wishes of Mrs Jackson to the very best of our abilities. We are deeply saddened that the courts have decided not to honour them." Mike Clarke, the RSPB's chief executive, said: "It is regrettable that, occasionally, courts need to become involved in interpreting the terms of a person's will."
David Bowles, assistant director of the RSPCA, said: "This court decision goes against a person's desire to give their money to whomever they wish. We hope that this does not stop others continuing to give money to help suffering animals."
