Congonhas recently repaved one of its runways after officials tried to ban wide-bodied jets from the airport on fears they could skid off its short landing strips.
The airport reopened on Wednesday, using an auxiliary runway.
"It was an announced tragedy, an accident in waiting," said Sandra Assali, president of the Brazilian association of friends and relatives of air crash victims.
The TAM accident is likely to renew pressure on President Luiz Inacio Lula da Silva to tackle safety concerns in Brazil's chaotic aviation system. Critics say his administration has been dragging its feet.
Lula declared three days of mourning and ordered an investigation. Pope Benedict, who visited Sao Paulo in May, said he was praying for the victims, the Vatican said.
"When is the next (accident) going to be?" Folha de Sao Paulo newspaper asked in its online edition on Wednesday.
A major air accident in September last year threw Brazil's aviation system into disarray, exposing a series of problems including a lack of air traffic controllers and equipment.
In that accident, 154 people were killed when a Brazilian Boeing 737 clipped wings with a private jet and crashed in the Amazon jungle in what was then the country's worst air disaster.
Controllers went on strike to protest poor pay and what they called spotty radar and radio coverage.
As a result, flights have frequently been canceled or delayed and irate passengers have stormed airline counters in protest.
A congressional inquiry is investigating aviation security and accusations that directors at the national airports authority took bribes from contractors.
