Around two million people had responded online to the joke "Storm Area 51, they can't stop all of us" event to "see them aliens".
Events in the Nevada desert - which took place mainly at two rural towns, Rachel and Hiko - were mostly festive, with crowds numbering in the low thousands and few arrests, officials said.
Three people were arrested on Friday at the remote once-secret military base, Lincoln County Sheriff Kerry Lee said, bringing the tally of accused trespassers to five since Thursday during events dubbed 'Alienstock' and 'Area 51 Basecamp'.
Several minor injuries were reported, and one man was treated for dehydration by festival medics in Rachel before returning to the party.
While costumed space aliens were a common, no one reported seeing actual extraterrestrials or UFOs.
"There's a great sense of community among everyone here," said John Derryberry, who drove with his girlfriend, Sarah Shore, from Nashville, Tennessee.
Almost 100 people went at 3am local time on Friday to the best-known "back gate" of the legendary former top-secret US Air Force base, near Rachel, and another 40 made a more difficult trek to a lesser-known gate in Tikaboo Valley, Sheriff Lee said.
During the day, about 300 went to the Tikaboo gate and another 800 people made the dusty eight mile drive to the Rachel gate.
One woman, aged in her 60s and from California, was arrested after making it clear to sheriff's deputies, her husband and everyone around her that she was going to trespass no matter what.
"It was just something she wanted to do," the sheriff said.
Two men were arrested after military security officers found them in the mountains inside the perimeter of the base somewhere between the two gates.
The gates are marked by bright floodlights, cameras and, at the Rachel gate, a squat tan bunker building with blackout windows - all surrounded by razor wire.
The sheriff in neighbouring Nye County reported that about 40 people dispersed after "heated warnings" from officers about 3am on Friday near a base gate not far from a conspicuously green "Area 51 Alien Centre" about 90 minutes' drive west of Las Vegas.
Matty Roberts, a 20-year-old from Bakersfield, California, who sparked the Area 51 phenomenon with a late-night Facebook post in June, hosted a Thursday evening event at an outdoor venue in downtown Las Vegas - also using the Alienstock name.
Area 51 Basecamp featured music, speakers and movies on Friday and Saturday at the Alien Research Center in Hiko.