The case was further complicated after Parliament passed legislation preventing further claimants from the Atkinson proceedings.
However, Spencer fought on, and today was awarded $207,681.84 for pecuniary loss.
She was denied a payment for damages.
Tonight, Spencer said after years of battling she finally felt like her human rights had been upheld.
"We have been vindicated and I welcome the court's decision which will hopefully pave the way for others," she said.
"We feel the doors have finally been broken down and flung wide open for other intellectually disabled people and their parents."
Spencer, of Auckland, said she was endlessly grateful to Jim Farmer QC and his team who took the case for her after years of rejection.
"Although I kept knocking on doors and writing letters, no one wanted to know," she said. "I was told we were not a high profile group, that we were an anomaly. But my love for my son would not allow me to give in to the disease of politics, process, and bureaucratic inaction.
"I took my endless paperwork to Jim and bombarded him and his team with my story. Words cannot express my gratitude to them."
Spencer said she was going to celebrate tonight.
"Having achieved this result Paul and I are now looking forward to enjoying our human rights."
Chief Human Rights Commissioner David Rutherford paid tribute to Spencer's battle.
"Margaret Spencer has always said that she was fighting not just for herself and her son but for many families in the same situation, we are very grateful to New Zealanders like her who fight for human rights on all of our behalf," he said.
"Today's landmark judgment is a testament to the efforts people with disabilities and their families have put in over many years in battling a system that frequently fails to acknowledge and respect their rights.
"We welcome the court's order that the Ministry of Health should educate its staff about the importance of the human rights of disabled people and their caregivers. Public policies that uphold and promote human rights principles deliver better outcomes for all New Zealanders."
Fight for Paul
2001: Margaret Spencer writes a complaint to then Prime Minister Helen Clark about the discrimination against family members caring for their disabled children, saying they should be paid the same as non-family carers.
2007: Spencer repeats the complaint to the Human Rights Commission, which is already taking another similar case -known as the Atkinson proceeding.
2010: The Atkinson claim is upheld by the Human Rights Review Tribunal, finding that excluding payments to carers of disabled family members was discriminatory and in breach of human rights.
2012: The Court of Appeal upholds that decision after being challenged by the Ministry of Health.
2012: Spencer applies for family caregiver funding. The Ministry of Health refuses her.
2013: Spencer seeks a judicial review of that decision. At the same time, a new Public Health and Disability Act is passed . The ministry says it precludes Spencer getting relief from review. That decision is also challenged by Spencer.
2013: Chief High Court judge Justice Helen Winkelmann finds in Spencer's favour, and says the ministry acted unlawfully and in breach of her rights by refusing to consider her application for funding. She said Spencer was not precluded by the new Act from from applying for compensation for past discrimination. The Ministry of Health appeals.
2014: Spencer begins receiving payments of $14.25 per hour, for 29.5 hours a week, for Paul's care.
2015: Winkelmann's decision about compensation is upheld by the Court of Appeal.
2016: Spencer compensation case reaches the High Court. She is awarded $200,000 compensation.
