Around 1,000 people gathered near the city's famous Istiklal Avenue and Taksim Square where organisers had wanted to originally hold the parade.
The activists unfolded a large rainbow flag while a press statement was read out amid heavy security in the area.
But police then warned activists to disperse and used rubber bullets against some who tried to access Istiklal Avenue.
UN rights chief warns Indonesia over crackdown against LGBT community
Amnesty International in Turkey later said on Twitter that 11 people had been detained as it called on police to "immediately" release them. The human rights group also said tear gas had been used against some activists.
The Istanbul governorate told the organisers that officials "could not take steps to secure their safety and did not find it appropriate for the Pride Walk to take place", according to a statement from Istanbul LGBT+ Pride Week on Facebook late Friday.
The Istanbul governor's office issued no public statement about the event.
"The governor cited the excuse of security in its decision to ban the march and in one word, this is comical. Our marches went on peacefully without being banned for 13 years," the organisers said in a press statement on Facebook hours before the march.
"We LGBTI+ (lesbian, gay, bisexual, transgender, intersex) are here with our pride despite all vain attempts to prevent us and we do not recognise this ban," they added.
"People are not afraid, shopkeepers are not afraid. However, the governorship is afraid, the police are afraid. They think that they can restrain freedom with the barricades they set up and the tear gas," one activist at the march.
The annual rally is the most important LGBT event in a Muslim country in the region.
Turkey riot police break up women's rights march
The Ankara governorate on Thursday banned a screening of the 2014 film Pride organised by the Communist LGBT group, saying such events could "incite hatred and enmity".
The governor's office added that there could be "danger to public safety".
The capital's governorate in November issued a ban on LGBT events but gay rights groups said they would take legal action against the order.
Although homosexuality is legal in Turkey, LGBT individuals frequently cite abuse and harassment.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ