Alejandro Dominguez said teams from Uruguay, Paraguay, Peru, Ecuador, Bolivia and Venezuela would take part in a qualifying series in January for the three vacancies.
"The Cup will start after the first week of January with home and away matches involving teams from Uruguay, Bolivia, Ecuador, Peru, Venezuela and Paraguay," Dominguez said in an interview at CONMEBOL headquarters outside the Paraguayan capital on Tuesday.
Mexico last month cited a clash of dates between a revamped Copa Libertadores, to be played throughout the calendar year from 2017, and their domestic league championships as a reason for withdrawing at least for a year.
"The (CONMEBOL) council dealt with Mexico's request, accepting to give them a year's sabbatical ... We will work with the Liga MX to see if there are possibilities of their return in 2018," Dominguez said.
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Mexico, the leading soccer nation from the northern CONCACAF region, have taken part in South America’s elite club competition since 1998.
"We'd have liked the Mexican teams to carry on taking part because they have never won the Libertadores and have only reached three finals but we have to worry about South America," Dominguez said.
"If they want to return they'll have to do so in 2018 and, if not, South America will still have the best football in the world."
CONMEBOL in September voted on modifications and an expanded number of teams in both its club competitions, the Libertadores and Copa Sudamericana, which is equivalent to UEFA's second-string Europa League.
Dominguez said it was still his dream to introduce a single Copa Libertadores final at a neutral venue like Europe’s Champions League, but some CONMEBOL member nations prefer the traditional two-legged decider, which will be retained at least for 2017.
The six countries entering teams in the January qualifying competition have three berths each in the 2017 tournament, whereas Brazil have seven, Argentina six and Chile and Colombia four each.
Colombian Libertadores holders Atletico Nacional and Chapecoense, who have been awarded the Sudamericana title after their team was all but wiped out in a plane crash last week, also have a berth each in a 44-team competition.
Modest Brazilian side Chapecoense were on their way to play Atletico Nacional in the first leg of the Copa Sudamericana final, the biggest match in the club's history, when their plane crashed killing 71 passengers.
Dominguez, who flew to Medellin to help in the aftermath of the crash, said CONMEBOL were talking to clubs about the best options for safe air travel to competition venues.
"There are clubs whose players have already asked not to travel by charter but with major airlines," he said. "That's something that isn't down to CONMEBOL itself but to each club.
"I don't think there is any sports body in the world or any private or public institution which needs to travel by charter that hasn't considered this situation."
(Writing by Rex Gowar, editing by Nick Mulvenney)
