The Disney Pixar film took $73.2m (£54.6m), while The Independence Day sequel took a disappointing $41.6m (£31m).
Blake Lively's shark thriller The Shallows did better than expected, taking $16.7m (£12.4m).
Filmed in Australia, it came in fourth and only cost $17m (£12.7m) to make.
On its opening weekend, Finding Nemo sequel Finding Dory had the most successful launch for an animated film in US box office history, taking $136.2m (£93.3m).
It is already the sixth-best selling film of 2016 after ten days with total takings of $285.6m (£214m).
That figure is less than $100m (£74.9m) short of the final total that Finding Nemo made.
Will Smith did not return to battle the aliens second time round in the Independence Day sequel but Roland Emmerich was back in the director's chair.
Bill Pullman, Vivica Fox and Jeff Goldblum reprised their characters, joined by new cast members Liam Hemsworth and Jessie Usher.
It cost $165m (£123.6m) to make and will need strong international ticket sales if it is to become profitable.
It has taken $102m (£76.4m) from 57 different markets since its release.
In third place was the Kevin Hart, Dwayne Johnson action comedy Central Intelligence.
It took $18.4m (£13.7m) in its second week and has now topped $69m (£51.7m) in 10 days.
Sony distribution chief Rory Bruer said social media buzz helped the film, which is about Lively's character battling for survival in a shark's feeding ground.
"We were able to convey that this is a movie that has you on the edge of your seat and is both fun and scary," he said.
Meanwhile, Matthew McConaughey's historical drama Free State of Jones took fifth spot.
The film, in which McConaughey plays the leader of a rebellion against the Confederacy, took $7.8m (£5.8m), which was below expectations.
It cost $50m (£37.4m) to make.

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29 July 2015 Last updated at 16:18 BST
Zion Harvey described waking up with new hands as "weird at first, but then good.'"
He lost his limbs due to a severe infection when he was two-years-old.
Zion had told his doctors and his mother that more than anything he wanted to be able to play on the jungle gym and throw a ball.
Four teams of surgeons worked over 11 hours to complete the complicated operation.

Halsey said on Twitter that he had "seen an incident and been told to say I haven't seen it".
He spoke out after Manchester City's Sergio Aguero received a retrospective three-game ban for violent conduct.
However, the Professional Game Match Officials Limited said: "There is no pressure to include or omit anything."
The body's statement continued: "Match officials submit their reports, including critical incidents, directly to the FA.
"Match officials ensure that their reports are a full and accurate description of the incident."
Halsey, who retired in 2013, also pointed out these were issues he had previously mentioned in his autobiography three years ago.
He later added: "To be fair to the FA... it's not them, it comes from within the PGMOL."
Formed in 2001, the PGMOL was established when referees turned professional and aims to improve standards across the Premier League, Football League and FA competitions in England as well as training and development.
Had the incident that saw Aguero banned by a Football Association panel for elbowing West Ham's Winston Reid been witnessed by a match official, including referee Andre Marriner, the retrospective punishment would not have been possible.
Former Manchester United captain Gary Neville said Halsey's claims were "too big" to avoid a full investigation.

The ISS recently was fitted with a high-definition projector, which the astronauts use for special movie nights, as well as video conferences with space scientists back on earth.
It is isn't the first time they have watched movies in space.
Commander Scott Kelly and her team used the same kit last month to watch space disaster movie Gravity.
Finding Dory has remained at the top of the US box office for a second week, as Independence Day: Resurgence came in second place.
[NEXT_CONCEPT]
An eight-year-old boy in America has become the youngest person to get a double hand transplant.
[NEXT_CONCEPT]
Former referee Mark Halsey's claims that he was told to lie after a game have been denied by the body which oversees match officials.
[NEXT_CONCEPT]
Astronauts have been watching Star Wars on board the International Space Station.