The three men, including the judge responsible for the case, were punished for "neglect of duty", state media say.
In another twist, the man's younger brother has surrendered to police, saying he was to blame for the 3.7m yuan (£350,000) fraud.
A retrial was ordered on Friday for Shi Jianfeng, after a huge public outcry.
At a news conference on Sunday, a higher court in Henan province announced the removal of the three officials from their posts.
It said a fourth official had been reprimanded, adding that the men had failed to investigate Mr Shi's case properly and there was insufficient evidence to convict him.
'Criminals in legal coats'
The 43-year-old farmer was found guilty last week of evading toll fees over a nine-month period while delivering sand and gravel in two trucks.
The court ruled he had used fake military number plates, meaning the vehicles were exempt.
However, Mr Shi had argued that he was being "manipulated by a relative".
On Saturday night, Shi Junfeng turned himself in to police in Yuzhou City, saying his brother had taken the blame for him.
It appears he had not thought his older brother would be sentenced so severely, telling police he had offered bribes to officials and had been assured he would be released quickly.
The case had generated a furious reaction online in China.
Many argued that far more lenient sentences are usually given for more serious crimes. There were also complaints that road tolls, required on most major highways, are too high for ordinary people to be able to afford.
An opinion feature in the Global Times newspaper said the "exorbitant tolls, rather than the man's bad behaviour" provoked the outcry.
The newspaper says those who set toll fees are referred to by some as "criminals in legal coats".