"I do not celebrate or feel pride in our having to ban Donald Trump from Twitter, or how we got here," he wrote.
"After a clear warning we'd take this action, we made a decision with the best information we had based on threats to physical safety both on and off Twitter."
He said he believed the ban was the right decision.
"We faced an extraordinary and untenable circumstance, forcing us to focus all of our actions on public safety," he said.
"Offline harm as a result of online speech is demonstrably real, and what drives our policy and enforcement above all."
Mr Dorsey wrote that banning an account has "real and significant ramifications".
"While there are clear and obvious exceptions, I feel a ban is a failure of ours ultimately to promote healthy conversation.
"And a time for us to reflect on our operations and the environment around us."
He conceded such a ban sets a dangerous precedent.
"The check and accountability on this power has always been the fact that a service like Twitter is one small part of the larger public conversation happening across the internet," Mr Dorsey wrote.
"If folks do not agree with our rules and enforcement, they can simply go to another internet service."
Mr Dorsey said he did not believe the other bans Mr Trump faced from Facebook, Instagram, YouTube and others were co-ordinated.
"More likely: companies came to their own conclusions or were emboldened by the actions of others," he said.
"This moment in time might call for this dynamic, but over the long term it will be destructive to the noble purpose and ideals of the open internet.
"A company making a business decision to moderate itself is different from a government removing access, yet can feel much the same."
Mr Dorsey said Twitter was funding an initiative to create a decentralised standard for social media.
"The efforts to censor, cancel and blacklist our fellow citizens are wrong, and they are dangerous," he said.
"What is needed now is for us to listen to one another, not to silence one another."
He did not make specific mention of his own accounts being deleted from Twitter, Facebook and Instagram after his posts were deemed to be encouraging violence.
Meanwhile, Mr Trump will be permanently banned from Snapchat when he leaves office.
The social media giant had suspended Mr Trump's account indefinitely last Wednesday, but Axios reports the account won't be reactivated.
Snapchat was the first of the social media companies to lock Mr Trump's account, citing breaches of its policies against spreading hate and encouraging violence.
Snapchat is not considered one of Mr Trump's preferred social media platforms, but his campaign used it regularly in an attempt to reach out to younger voters.