Biden has the right of veto over US International Trade Commission (ITC) decisions, but it is rare for it to be done. US Trade Representative Katherine Tai decided not to recommend overturning the ban after talking to the ITC.
The ITC order kicks in on 26 December stopping Apple Watches that use a feature that measures blood-oxygen levels from entering the country.
Apple has been using the feature in its smart watches since its Series 6 model in 2020.
Apple can challenge the ban in the US Court of Appeals for the Federal Circuit. The company has stopped selling its Series 9 and Ultra 2 smartwatches in the US since last week.
The ban does not affect Apple Watch SE, a cheaper model, which will still be sold.
Masimo, the medical company, has accused Apple of poaching its staff, nicking its pulse oximetry technology and jacking it under the bonnet of the Apple Watch.