She roared into the heavens a fortnight ago atop a column of fire, enthralling a million spectators as she set off on her final voyage. But the space shuttle Atlantis slipped quietly back to port on Thursday at the end of her five-million-mile journey, gently lowering the curtain on three extraordinary decades of adventure in human space flight.

Nasa's space shuttle era officially came to a close at 5.57am (10.57am BST) when the orbiter and its crew of four astronauts touched down at a remote runway in the northern reaches of Florida's Kennedy Space Centre in Florida, watched by a few hundred space agency workers and reporters who turned out before dawn to witness a moment of history.

Like a ship's bell ringing a vessel safely back home, two deafening sonic booms pierced the Florida sky to signal Atlantis's otherwise silent arrival, and the last few seconds of the 135th and final mission since the first launch of Columbia in April 1981.

It was day of celebration and raw emotion, with Nasa employees openly weeping on the runway in front of the newly retired shuttle, and Chris Ferguson, the Atlantis commander, paying a moving tribute to it and the rest of the spacecraft fleet.

"The space shuttle has changed the way we view the world and it's changed the way we view our universe," he said moments after landing.

"There are a lot of emotions today, but one thing is indisputable. America's not going to stop exploring. Thank you Columbia, Challenger, Discovery, Endeavour and our ship, Atlantis. Thank you for protecting us and bringing this programme to such a fitting end."

Charles Bolden, a former astronaut who is now the Nasa administrator, was keen to look ahead. "At today's final landing of the space shuttle, we had the rare opportunity to witness history," he said.

"We turned the page on a remarkable era and began the next chapter in our nation's extraordinary story of exploration. This final shuttle flight marks the end of an era, but today we recommit ourselves to continuing human spaceflight and taking the necessary and difficult steps to ensure America's leadership in human spaceflight for years to come."

Despite the rallying words, many feel that the moment of wheels-stop for Atlantis also marked the end of a half-century of US dominance in space.

For the first time in the agency's 53-year history it has no vehicle, existing or in the works, capable of launching astronauts into orbit. The International Space Station, built almost exclusively by American astronauts flying shuttles, must now be serviced by Russia's Soviet-era Soyuz spacecraft.

More humiliating is that Nasa is having to hitch rides to the space station with the Russians, paying them up to $63m (£39m) for each astronaut it wants to send.

Private companies including SpaceX, Lockheed Martin and Sierra Nevada have won Nasa contracts to develop spacecraft to compete for such lower Earth orbit duties and hope to be flying humans to the ISS by 2015. Nasa, meanwhile, is charged with designing, but not yet building, a new heavy-lift rocket that might eventually take astronauts back to the moon for the first time since 1972, and perhaps later on to Mars.

President Barack Obama, who cancelled the planned next-generation Constellation programme of spacecraft and rockets on cost grounds, is under pressure to announce a date when work on the so-called Space Launch System can begin.

Bob Cabana, the Kennedy Space Centre director, admits the agency faces a severe challenge. Almost 10,000 workers have lost their jobs with the end of the shuttle programme and last week the influential house appropriations committee in the US Congress announced it wanted to slash Nasa's budget by $1.9bn.

"We enjoy this celebration and reflection on everything the shuttles achieved, but we go straight back to work on Monday," Cabana said.

"We have to put the architecture into place to support the heavy-lift rocket that will allow us to get back to exploring. It's in our DNA to explore; we need to be doing it."

Nasa's retired shuttles are to go on public display. Atlantis, which travelled almost 126m miles in its 33 flights since its first launch in October 1985, will be housed at the space centre's visitor complex after a lengthy decommissioning process.

Endeavour, which completed its final flight on 1 June, is heading for the California Science Museum in Los Angeles and Discovery, last flown in March, will replace the non-orbiting shuttle prototype Enterprise at the National Air and Space Museum in Washington DC.

Nasa's two other shuttles, Challenger and Columbia, were destroyed in flight during missions in 1986 and 2003 respectively, each disaster costing seven astronauts their lives. In all, the five shuttles flew 542m miles, including missions to release satellites and launch and repair the Hubble space telescope.

Mike Leinbach, Nasa's launch director, remembered the sacrifices made by the crews and paid tribute to the generations of employees who worked on the shuttle programme.

"There's a lot of sadness that it's over, and it's hard to say goodbye to so many people who have over the years become family," he said. "But the sun will rise again tomorrow."

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