US ally Noboa had caused an outcry by earlier saying a base could be erected on Baltra, a small island in the Pacific archipelago chain, to combat drug and fuel trafficking and illegal fishing.
The Galapagos, where British naturalist Charles Darwin developed his theory of evolution, hosts plant and animal species found nowhere else in the world.
On Friday Noboa said: "Baltra is ruled out," in a decision taken with US Homeland Security Secretary Kristi Noem.
Alternative sites were identified at be Manta or Salinas -- coastal cities on the mainland where "there is a higher priority in terms of arms trafficking, fuel trafficking, and drug trafficking," Noboa told Teleamazonas.
At the president's initiative, Ecuadorans will decide in a referendum on November 16 whether to repeal a 2008 constitutional ban on their country hosting foreign military bases.
Baltra, which has an airport, was home to a US military base during World War II.
The United States for years operated a military base in the Pacific port of Manta.
In 2009, then left-wing president Rafael Correa, a fierce US critic, refused to renew the lease.
Plans for a new base come as the United States ratchets up strikes on alleged drug-smuggling boats off South America that have so far claimed at least 62 lives.
Ecuador has in recent years become a hub for cocaine trafficking.
On a visit to Quito in September, US Secretary of State Marco Rubio vowed to help Noboa "wage war" against drug-trafficking "terrorists."
The Galapagos Islands, a World Heritage Site, are situated some 1,000 kilometers (620 miles) off the coast of Ecuador.
The Ecuadoran armed forces regularly seize drugs, weapons and fuel in the surrounding waters.
Noboa said Ecuador has also held talks with France and the United Kingdom about "the importance of having a (foreign military) presence at the border" with Colombia -- the world's largest cocaine producer.
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