The move came as a woman with H1N1 in the US state of Texas died on Tuesday, although the authorities did not confirm that the virus was the cause of her death.
Agustin Carstens, the Mexican finance minister, said on Tuesday his country would introduce a $1.3bn stimulus plan to help the economy, which was hit hard by the crisis.
The nationwide shutdown and the effect on the tourism industry caused a loss of about $2.3bn, or "close to 0.3 per cent" of gross domestic product, he said.
Carstens said the government would launch a marketing campaign to lure back tourists and offer $380m in credits and subsidies for companies.
High schools and universities were also to begin classes on Thursday, while primary schools will resume lessons next week.
But cinemas, theatres and nightclubs remain closed until further notice.
Felipe Calderon, the Mexican president, said the world should thank Mexico for its response to the new strain of flu.
"The frontline of the battle was Mexico, and we defended all of humanity from the propagation of this new virus," he said.
Mexico flew dozens of its nationals home from China on Tuesday, after they were quarantined by Beijing in a move the Latin American country criticised as unfair and discriminatory, sparking a diplomatic row.
A Chinese aircraft sent to Mexico to retrieve its citizens was set to return on Wednesday.