The findings, published Thursday in the journal Nature, will help guide a NASA mission en route to the planet and should yield insight about the relationship between planets and their moons, say scientists involved with the project.
Weaver is the project scientist for NASA's New Horizons mission, which is slated to reach Pluto in 2015.
"This gives us further support that a giant collision took place at the beginning of the solar system," he added.
The location of the moons — designated S/2005 P1 and S/2005 P2 — in the Kuiper Belt could help answer questions about the relationship of the Earth to its moon, Weaver said.
The Kuiper Belt, where a possible "10th planet" was discovered last year, is an enormous band of icy, rocky objects beyond Neptune that scientists have begun to understand only in the past decade.
"If we want to understand the process by which planets and moons are formed, we need to understand both [Pluto's and Earth's] systems," Weaver said.
The moons, whose existence was confirmed Feb. 15, were first spotted last year in a stroke of serendipity.
Weaver, who was also working on a separate NASA mission, asked Max Mutchler of the Space Telescope Science Institute in Baltimore to assist him in examining photographs taken by the Hubble Space Telescope.
Mutchler, an expert with Hubble data, found evidence of the moons within a day — but by accident.
"They were sort of playing this game of peek-a-boo — jumping in and out of a strip of missing data," Mutchler said. "[The search] was almost an afterthought. It wasn't even a priority. The moment I discovered them, I wasn't even searching, to be honest."
Another twist is that the discovery never would have happened if the telescope had worked correctly. A Hubble panel rejected the idea initially, Weaver said, but then approved it when an instrument failure scrapped other projects.
Subsequent observations have confirmed that the moons orbit on the same plane as Pluto's other moon, Charon, which was discovered in 1978.
"Little pieces of evidence kept coming out in our favor and making the case," Weaver said. "The two moons are almost exactly where we'd predicted they'd be."
Pinpointing an object in the outer limits of the solar system is like finding an artifact older than anything on Earth, Mutchler said.
"It's almost like a cryogenic preservation chamber of what the solar system was like 4 billion years ago," Mutchler said of Pluto. "It's a great way to get insight into the formation of the solar system."
Scientists know little about the moons beyond their existence.
On March 2, the team will peer at them again through Hubble's lens, hoping to decipher their nature, general shape and rotation rate, Weaver said.
The closest observations are still nine years away, when the moons will be photographed in detail by the New Horizons probe.
Besides knowledge, a perk of discovering a heavenly body is naming rights, and the team will submit a nomination to the International Astronomical Union within a month, Weaver said. For now, he and fellow researcher Alan Stern of the Southwest Research Institute in Boulder, Colo., have pet names for the moons: "Baltimore" and "Boulder."
The researchers will almost certainly follow tradition by selecting a name from the underworld of Greek mythology, Weaver said.
Pluto, also known as Hades, was the Greek god of the underworld. Charon — the name of the Greek boatman who ferried souls to hell — was chosen by discoverer James Christy in honor of his wife, Charlene.
"We'd like to name them after our wives," Weaver said, "but I don't think that's going to happen."