The firm also announced another new console, Project Scorpio, which will offer virtual reality and 4K gaming.
It will be released by Christmas 2017 but no details of a price were given.
The Xbox One S, however, will cost $299 (£210) and include support for High Dynamic Range (HDR) gaming, with extra levels of brightness and more colour.
Pictures of the device, which will also include 4K DVD and Blu-Ray playback, were leaked ahead of E3.
One analyst said many gamers might not be ready to buy a new console so soon after the Xbox One's release.
It's an unusual move to release a new version of a console "mid-cycle", or before a completely refreshed device is launched, according to games industry analyst Ed Barton of Ovum.
"We are in slightly uncharted waters," he told the BBC ahead of Microsoft's E3 event. "There's a risk of the market already being saturated."
However, Sony will also launch an upgraded version of its PS4 console in early 2017.
Piers Harding-Rolls at analysts IHS pointed out the earlier release date for the Xbox One S could give it the edge in terms of sales.
Although much was made of the new consoles' abilities, Microsoft made no mention of its upcoming augmented reality headset, Hololens.