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.
Finding Dory has remained at the top of the US box office for a second week, as Independence Day: Resurgence came in second place.