Tesla Inc. stopped online sales of the $35,000 base version of its Model 3 compact weeks after introducing it, the latest shift in sales tactics as the electric-car maker struggles to deliver long-promised affordability and avoid losing money.

Customers can still order the $35,000 version of the car by telephone or in Tesla’s network of stores, the company said. But the lowest-priced option available online is now an upgraded Model 3 that will cost $39,500, or nearly 13% more than the base version.

The...