His comments at an event at the SNP party conference in Perth, echo the pledge by Deputy First Minister Nicola Sturgeon, when she announced the plans to take the Ayrshire airport into public ownership.
Keith Brown said acquisition was the only option to prevent closure and to protect thousands of jobs linked to the facility.
He said: "It is not the Scottish Government's business to go around buying airports but, given the consequences of not taking action for job losses and the economy, it was the right decision when no-one else was left standing to buy it."
The minister said he was aware of Glasgow's concerns.
He added: "We will have regard for the other airports with anything we do with Prestwick. We have already met with Glasgow and Heathrow airports."
Mr Brown said it had not yet been decided what role Prestwick would play and mentioned its potential use as a contingency airport or freight hub.
He said: "There are a number of things we could do but it is a challenge."
Mr Brown was speaking at an event hosted by Heathrow Airport to promote its plans for expansion.
The transport minister said he was concerned about the limited number of flights from Glasgow and other Scottish airports to Heathrow, affecting the ability to connect with the wider world.
Heathrow director of policy Nigel Milton said the UK could only sustain one major hub airport and Heathrow was best placed to continue that status.
He said: "If you had two hub airports it would split the transfer business and long-haul flights would become unviable. Scotland can't support the long-haul flights to the emerging economies, like Brazil, Russia, India and China. It is an inconvenient truth."
Mr Milton said Heathrow was not a London airport but served Wales, England, North-ern Ireland and Scotland.
However he was told of concerns that landing slots were going to more lucrative long-haul flights at the expense of domestic transfers.
Mr Brown said that if Heathrow couldn't offer enough space for flights from Scottish airports there were other hub airports. He added: "There is a threat (to Heath-row) from Istanbul and the hub for the west of Europe could be Schipol. My message to Heathrow is make yourself more relevant to Scotland."