"Privacy is a fundamental human right," said Apple's software chief Craig Federighi.
He said that there will be an option for apps which request location information to have to ask every time they require it, and they will be blocked from using other markers, such as identifying Wi-Fi or Bluetooth signals.
Apple is also launching a sign-in-with-Apple login, as an alternative to logging in to a service using a social media account.
Using this login, users can choose to hide their email address, with Apple creating a random alternative address which will forward to the real mailbox.
"The unveiling of 'Sign-in With Apple' will concern rivals, particularly the web giants," commented Ben Wood from CCS Insight.
"Existing sign-in services provide a simple means for single sign-in across the web. Privacy is the differentiator that will be heavily emphasised versus Facebook and Google, and represents a great marketing tool for Apple's broader privacy stance."
The next iteration of the iPhone's operating system - iOS 13 - includes a range of changes to its interface, as well as new functions.
The new Dark Mode enables iPhone apps to be viewed with a black background, while the Apple Maps app will come with a virtual tour experience similar to Google's Street View.
Other key features include the option to silence unknown callers and block senders within the Mail app, improved search in messages, and optimised battery charging.
Apple has also made improvements to its language keyboards, including the introduction of new bilingual keyboards and typing predictions for Arabic, Hindi, Thai, Cantonese, Vietnamese and the 22 official Indian languages.
Other news from the conference included:
The Find My iPhone and Find My Friends apps will now track and locate any Apple device, even if it is offline
Apple says it travelled 4 million miles by car and aeroplane in order to improve the detail on its maps app
The new Apple TV screensaver will feature 4K high definition images from under the ocean filmed in collaboration with the BBC Natural History Unit, which made Blue Planet
Improvements to Apple's Memojis - a form of 3D avatar - were demonstrated in a video made by beauty vloggers Desi Perkins and Patrick Starrr. They now include more accessories such as piercings and make-up
The Apple Watch is to become more independent from the iPhone with its own app store.
New apps for the Watch include a menstrual cycle tracker, with an optional fertility window predictor, and a noise level tool to alert Watch wearers when they are around noise levels that can damage hearing.
Apple said it would not record or store the noise data.
The tech giant also unveiled a redesigned Mac Pro complete with a 28-core Intel processor and 6k retina display screen, which is 40% larger than the current iMac display screen.
It will launch in the autumn with prices starting at $5,999 (£4,700) - this does not include the screen or stand.
And instead of buying additional monitors, existing Mac users will now be able to use the iPad as a second screen.
Tuong Nguyen, senior principal analyst at Gartner, said this year's event had a different feel to its predecessors, following on from Apple's last announcements which saw it reposition itself as a provider of services, rather than hardware.
"Typically at WWDC you might see it begin with something interesting, in terms of how devices are used or how apps interact, but this time it kicked off with a video that looked more like a movie trailer," he said.
"Is this the new way we should see Apple events, more rooted in the media content side of things, rather than the strong emphasis on technology and hardware innovation?
"Remember, the last event was all about services and content - this may be the new way that Apple differentiates itself."