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Brazil crisis: Rousseff impeachment vote 'annulled'
In his decision, Mr Maranhao said there had been irregularities during the lower house session in which its members overwhelmingly voted in favour of the impeachment process going ahead.
He said members of the lower house should not have publicly announced what their position was prior to the vote, and that it had been wrong of party leaders to instruct their members how to vote.
Mr Maranhao called for a new vote in the lower house, but it is not yet clear whether the senate will agree to return the proceedings to the lower house.
It is also not known whether Mr Maranhao's decision can be overruled.
'Political fiasco', Wyre Davies, BBC News South America correspondent
When I sat down for an extended interview with Dilma Rousseff in Brasilia last week, she was fully prepared for and anticipating her likely suspension as president.
She assumed, like just about everyone else in Brazil, that the country's Senate would vote in favour of a full impeachment trial.
Indeed, Ms Rousseff told me she would fight to clear her name after her expected suspension from office later this week over charges that she illegally hid the scale of the budget deficit.
The decision by the interim speaker of the lower house to annul the impeachment process took everyone - including the president - by surprise.
But if it is a stay of execution for Ms Rousseff it may only be temporary.
The case has already left Waldir Maranhao's jurisdiction and is before the Senate where senior figures have already vowed to ignore the ruling from Mr Maranhao.
Whatever the outcome - and don't bet against the impeachment process getting "back on track" - this fiasco does the image of Brazil and its discredited political system no good.
An increasing majority of Brazilians are not just dissatisfied with the country's situation in general but, in particular, with the behaviour of politicians in Brasilia.
The place is, rightly or wrongly, perceived to be riddled with corruption where politicians serve only in their self interest while the rest of the country struggles with a worsening economy, an ever more violent society and with the country's image being ridiculed overseas.
Mr Maranhao, who opposed the impeachment process in the 17 April vote, only took over as the speaker of the lower house last week, after the previous speaker,Eduardo Cunha, was suspended.
Mr Cunha, an outspoken critic of President Rousseff, led the impeachment drive against her.
Reacting to the news, Ms Rousseff urged "caution", adding that there was a "hard fight ahead".
The BBC's South America business correspondent, Daniel Gallas, says it is unlikely that the 367 members of the house who voted in favour of the impeachment process - many of whom gave impassioned speeches before casting their votes - will change their minds.
Ms Rousseff has said the efforts to impeach her amount to "a coup attempt".
She has accused Mr Cunha and Vice-President Michel Temer of being the "ringleaders of the coup".
Mr Temer would step in as interim president if Ms Rousseff were to be suspended from office.