However, he expressed sadness at what he described as the "extraordinary and untenable circumstances" surrounding Mr Trump's permanent suspension.
He also said the ban was in part a failure of Twitter's, which hadn't done enough to foster "healthy conversation" across its platforms.
Twitter has been praised and criticised for freezing Mr Trump's account.
German leader Angela Merkel and Mexican President Andres Manuel López Obrador - neither an ally of the outgoing US president - spoke out against the tech titan's move.
In a long Twitter thread, Twitter's chief said he did not celebrate or feel pride in the ban - which came after the Capitol riot last week.
He reiterated that removing the president from Twitter was made after "a clear warning" to Mr Trump.
"We made a decision with the best information we had based on threats to physical safety both on and off Twitter," Mr Dorsey said.
He also accepted that the move would have consequences for an open and free internet.
"Having to take these actions fragment the public conversation. They divide us….And sets a precedent I feel is dangerous."
He also addressed criticism that just a handful of tech bosses can make decisions on who does and doesn't have a voice on the internet - and on accusations of censorship.
"A company making a business decision to moderate itself is different from a government removing access, yet can feel much the same," said Mr Dorsey.
The decision to remove users, posts and tweets has been criticised by some for violating First Amendment - free speech - rights.
However Big Tech generally argues that as they are private companies, and not state actors, the law does not apply when they moderate their platforms.