The authorities had ordered a five-day nationwide shutdown on Friday in an attempt to halt the spread of the virus.
Al Jazeera's Mariana Sanchez in Mexico City says the city of 20 million is now getting back on track following the crisis, with businesses reopening, although the city has lost about $2.2bn in revenue in the past five days.
However many places will remain closed - including universities, high schools, primary schools and churches - until at least Thursday, until authorities are absolutely sure the spread of the virus has been contained, our correspondent says.
Agustin Carstens, the Mexican finance minister, said on Tuesday a $1.3bn stimulus plan would be introduced to help the economy.
Carstens said the government would launch a marketing campaign to lure back tourists and offer $380m in credits and subsidies for companies.
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 returned on Wednesday.