His centre-right party is embroiled in a judicial probe into claims it misused European Union parliamentary funds, and its importance as a Macron ally waned after his Republic on the Move (LREM) party won a big majority in Sunday's parliamentary election.
Center-right Prime Minister Edouard Philippe remains at the head of the government.
Goulard is a member of Modem, the centrist party that allied itself to President Emmanuel Macron's party in the presidential and legislative elections, but which now faces an inquiry over the way it hired parliamentary assistants in the European parliament, AFP reported.
The new Cabinet has 28 members, half of them women and half men, up from the 22 appointed after Macron's election last month.
But she said the possibility of an investigation made it hard for her to stay in the post given Macron's agenda to clean up politics.
MoDem's departure, however, risks unbalancing Macron's carefully crafted government of the left, right and centre, which broke with convention as he extended his support base.
Mr Bayrou announced his resignation following allegations of misuse of European Parliament funds by the centrist party he founded, the Modem.
Even more embarrassing for Macron is that his justice minister was in the process of promoting a law to clean up politics, a key policy promise of the recently elected president.
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"It simplifies things", government spokesman Christophe Castaner said on Europe 1 radio.
Marine Le Pen, the leader of the far-right National Front who lost to Macron in the presidential election, said Bayrou had been discarded because he was no longer any use to the president.
In a press conference on Wednesday, Bayrou said he didn't want to "expose" Macron and the government to "lying campaigns".
On Monday, Richard Ferrand, minister for territorial cohsion and the general secretary of Macron's fledgling political party La République en Marche (La REM - Republic on the Move) resigned after he was put under preliminary investigation for nepotism and financial impropriety.
The opposition Republicans called the resignations a "political scandal" and a "major government crisis".
Bayrou himself had announced plans to ban lawmakers from hiring family members, one of a raft of proposals under Macron's bid to clean up politics.
First Lady Brigitte Macron, a former drama teacher, met a group of teenage students preparing to play at the presidential premises for France's annual music festival and told them of her piano-player husband's musical talents.
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