Constructors completing the project have admitted they will not finish the intended design until after the tournament but the event's local organising committee have stressed this will not be a problem.
The Itaquerao Stadium will host the opening match between Brazil and Croatia on June 12 before England face Uruguay there a week later.
On Sunday it underwent its final test by staging a Brazilian league match between Corinthians and Figueirense, which was affected by rain and hail storms forcing those among the restricted crowd of 40,000 not under cover of the roof to seek shelter elsewhere.
"The only aspect of the roof which will be unfinished is the inner liner, not impacting the effective protection of the stands," said the local organising committee in a statement to Press Association Sport.
"A glass finishing will also not be concluded, which similarly does not jeopardise the effectiveness of the roof.
"It is important to highlight that there is no obligation, neither from FIFA nor from the local organising committee, that FIFA World Cup stadia offer roofs protecting 100 per cent of the stands.
"Therefore, the architectural design of Arena de Sao Paulo, as well as of all other 11 stadia, does not guarantee that all the public will be immune to rain, which would be possible only in indoor arenas.
"Likewise, it was never foreseen in the project that the complementary stands had roofs."
A league match was also held at Arena Pantanal in the western city of Cuiaba on Sunday, meaning all venues have now undergone pre-tournament tests.
The Itaquerao Stadium, which will have a capacity of nearly 70,000 when it holds the tournament opener, has been dogged by problems since construction, the cost of which has rocketed from £95million to an estimated £320million, began in 2011.
Earlier this year a worker died while installing some of the 20,000 temporary seats required for the opening game, prompting officials to briefly halt construction after two previous fatalities at the venue late last year when a crane collapsed.
While the stadium itself is now operational, reports suggest there is a lot of work still do to outside the venue in relation to infrastructure.
- Sports & Recreation