The decision on Sunday to send Imamoglu to jail comes after the main opposition party, European leaders and hundreds of thousands of protesters criticised the actions against him as politicised and undemocratic.
As the courtroom developments unfolded, there were signs that the mayor's troubles were galvanising opposition against Erdogan's government, which has run Turkey for 22 years.
Nearly 15 million Republican People's Party (CHP) members and non-members, who made up the vast majority, streamed into polling stations nationwide to either elect or endorse Imamoglu as its candidate in a future presidential vote, the party said.
The non-member vote - more than 13 million, according to the CHP - could indicate that Imamoglu, 54, enjoys wide public support beyond the party faithful. The party's chairman said it showed the need for early elections.
Imamoglu has denied the charges he faces as "unimaginable accusations and slanders" and called for nationwide protests on Sunday.
"We will rip away this coup, this dark stain on our democracy, all together," he said.
Footage showed him being taken to Silivri prison in a police convoy after the ruling. The mayor of Turkey's largest city was also removed from duty, along with two other district mayors, the interior ministry said.
The government denies that investigations are politically motivated and says courts are independent.
Turkey's vice president, Cevdet Yilmaz, and Central Bank Governor Fatih Karahan sought separately to calm market jitters that sparked a sharp selloff in Turkish assets since Imamoglu was detained last week, and that analysts expect to accelerate after his jailing.
A nationwide ban on street gatherings was extended on Saturday for four more days but protests, scattered skirmishes with police and some detentions continued in major cities on Sunday, the fifth night of mostly peaceful anti-government demonstrations.
The court said Imamoglu and at least 20 others were jailed as part of a corruption investigation, one of two opened against the two-term mayor last week.
It said he was arrested for "establishing and leading a criminal organisation, accepting bribes, embezzlement, unlawfully recording personal data, and rigging public tenders in connection with a financial investigation".
The jailing caps a months-long legal crackdown on opposition figures and the removal of other elected officials from office, in what critics called a government attempt to hurt their election prospects.
Six of the CHP's 27 municipal mayors in greater Istanbul are now under arrest - a year after municipal elections in which opposition parties handed Erdogan's AK Party its worst ever electoral defeat.
The CHP opened party polling stations on Sunday to non-members to cast "solidarity votes" for Imamoglu, who was the only name on the ballot for presidential candidate.
CHP Chairman Ozgur Ozel said the high turnout in the primary elections - 14.85 million total ballots cast for Imamoglu - was a strong rebuke to what he called a "coup attempt".
It called "Erdogan's legitimacy into question and makes an early election inevitable", he told crowds at a municipal headquarters in Istanbul.
"If they believe they can compete with us, with Ekrem Imamoglu, then let them call for an early election."
No general election is scheduled until 2028.
But if Erdogan, 71, who has led Turkey for 22 years, is to run again, parliament would need to back an earlier election since the president will have reached his limit by that date. Imamoglu is leading Erdogan in some opinion polls.
Imamoglu is also facing terrorism charges, but the court did not formally arrest him on those at the same time.
A future ruling to jail him pending trial on these charges could allow the government to appoint a trustee to run Istanbul. A conviction could prevent him running for president.
The CHP said it would appeal the ruling and elect someone to work as acting mayor. Shortly after the ruling, the mayor vowed to ultimately defeat Erdogan, and said those who ran the investigation would be held accountable.
"Imamoglu has become Erdogan's ... nightmare," Mehmet Karatas, an opposition supporter, said outside the courthouse.
"We will make Ekrem Imamoglu president."
