Supporters of the far-right president have erected hundreds of roadblocks across Brazil since it was announced that Mr Bolsonaro's left-wing rival Lula won the election.
Mr Bolsonaro said blocking roads was not a part of "legitimate" protests.
He encouraged people to choose other ways of demonstrating.
Many hardcore Bolsonaro supporters have refused to accept the result of Sunday's presidential run-off, which saw former president Luiz Inácio Lula da Silva narrowly win with 50.9% of valid votes.
Angry with the result, lorry drivers set up blockades across the country. They have so far lasted three days and have caused considerable disruption to the transport of goods, including food and fuel.
Police have struggled to contain all of the blockades, although the federal highway police said more than 700 had now been dismantled.
Addressing the blockades in a video posted on his Twitter account on Wednesday, Mr Bolsonaro said: "I know you are upset... Me too. But we have to keep our heads straight.
"I want to make an appeal: clear the roads," he said, adding that blocking roads "obstructs our right to come and go, which is in our constitution".
However, he encouraged protesters to find other means of demonstrating and welcomed the various rallies that have been held in his support, in which people have displayed Brazilian flags and chanted anti-Lula slogans.
Some have also called for military intervention to keep Mr Bolsonaro in power.
"This is very welcome and is part of democracy," he said.
Although Mr Bolsonaro has still not publicly conceded defeat, in a speech on Tuesday, he did not contest the election result either.
He also agreed to the transition of power in the speech, which Brazil's Supreme Court said shortly afterwards showed that he had recognised the result of the election.
Mr Bolsonaro's term as president will end when Lula is inaugurated as his successor on 1 January.
Lula, who previously served as president from 2003 to 2010, is now 77 and will become the oldest person to assume the post.
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