Dr Andrew Wakefield's 1998 Lancet study caused vaccination rates to plummet, resulting in a rise in measles - but the findings were later discredited.
The General Medical Council ruled he had acted "dishonestly and irresponsibly" in doing his research.
Afterwards, Dr Wakefield said the claims were "unfounded and unjust".
The GMC case did not investigate whether Dr Wakefield's findings were right or wrong, instead it was focused on the methods of research.
During the two-and-a-half years of hearings - one of the longest in the regulator's history - he was accused of a series of charges.
'Invasive tests'
It was alleged he carried out invasive tests on children which were against their best clinical interests and paid children £5 for blood samples at his son's birthday party.
The panel looking into the allegations said the case was proven on both counts.
In regards to the blood tests it ruled he had acted with "callous disregard for the pain they might suffer".
After the hearing Dr Wakefield said: "I am extremely disappointed by the outcome.
"The allegations against me and my colleagues are unfounded and unjust."
The GMC now has to consider whether Dr Wakefield's behaviour amounts to serious professional misconduct and then if any sanctions should be imposed, such as striking him off the medical register.
However, that ruling is not expected for some months. 
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