Queenslander Ron Williams said it was as much as he could have ever hoped for the ruling that Commonwealth funding of the program that was set up under the Howard government in 2007 was invalid.
"We achieved what we went to Canberra for," he told AAP as he headed home on Wednesday evening.
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"It was never correct that John Howard should have launched this clearly political manoeuvre all those years ago."
Four of Mr Williams' children attended the Darling Heights State School in Toowoomba, which has employed a chaplain under the program since 2007.
In 2010 he decided to challenge the program as unconstitutional and the full bench of the High Court heard his case in August last year.
The court ruled in a 6-1 majority that the way the program has been funded is invalid under scope of executive power in section 61 of the constitution.
As well as this argument, Mr Williams also challenged it on the grounds of section 116 of the constitution, which bans religious
tests for Commonwealth officers.
The court unanimously dismissed that position.
Mr Williams said he and his lawyers had known from early on that aspect of the case was unlikely to go far because no law had been made to establish the program.
But he believed the question still needed to be raised.
"The separation of church and state matter, that's what led us to the constitution," he told AAP.
"I would expect the reason there was no legislation made in the first place to legitimise this funding is because it would have crossed over the line in the (religious test) establishment cause."
The federal government says it is still committed to the chaplaincy program and will work out how to let funding to still flow to schools.
"It is clear that there is a cure for each of these problems whether it's particular legislation, whether it's payments through
the states," Attorney-General Nicola Roxon said.
Mr Williams was a bit disappointed the government's first reaction was to find some workaround.
"But we'll see where it all goes and whatever they do is what they do," he told AAP.
"I now have an enormous support base of concerned parents and citizens and teachers, and people of faith as well."
Many of those had donated to help raise about a third of his legal costs.
"It was quite incredible and heartwarming," Mr Williams said.
