Figures issued by the Federal Electoral Tribunal after assessing 375 complaints showed Calderon's advantage over leftist Andres Manuel Lopez Obrador dropped from about 244,000 votes to 239,751.
The seven judges decided to scrap 81,080 votes in favour of Mr Calderon and 76.897 for his rival.
The tribunal is yet to formally rule on the validity of the July 2 balloting and must announce a president-elect by September 6.
Mr Lopez Obrador, a popular former Mexico City mayor and standard bearer of the Party of the Democratic Revolution (PRD,) claims massive fraud marred the elections.
But Mr Calderon, of the ruling National Action Party (PAN,) insisted he had clearly won the vote in what authorities said were the closest elections in Mexico's history.
Electoral authorities had rejected Mr Lopez Obrador's demand for a full recount of the 41 million votes, but conducted a new tally of nine percent of the ballots earlier this month.
The fiery leftist said on Sunday the election results should scrapped altogether, and claimed Mexico's institutions "were in crisis, in ruins, worthless."
Independence day
But Mr Lopez Obrador and his followers were expected to abide by the court's verdict as failure to do so could lead them to lose their status as political parties as well as public funding.
On September 16, they plan to hold a "democratic national convention" to discuss strategy in downtown Mexico City.
The meeting will coincide with celebrations marking national independence day.
In an interview with Le Monde newspaper last week, Mr Lopez Obrador said the convention could go so far as to proclaim him president.
"The assembly could also to decide to name a legitimate president, a head of government or a coordinating committee for civil resistance," he said.
A spokesman for Mr Lopez Obrador's Common Good coalition said the dispute with the ruling party was "a confrontation between two Mexicos."
"One of them is represented by the government, corporate world and the big media that make decisions every day. On the other side are the people, who vote once every six years. We have decided to respect their choice," he said.
International observers said they were satisfied with how the July 2 poll was organised and conducted.
The new president takes over from incumbent on December 1 for a six-year term.