Yes, the Narva-Ivangorod border checkpoint is one of those designated for e-Visa holders (source: https://en.wikipedia.org/wiki/Visa_policy_of_Russia).
The fact that you'll be entering from the EU / Schengen Area is not a problem. Russia's borders with EU countries are officially open and anyone with a valid visa (or a visa-exempt passport) is admitted. However, if you plan to return back to the Schengen Area, make sure your Schengen visa allows multiple entries.
As always in case of Russia, it's advisable to reserve plenty of time for the border formalities. Russian officials can subject you to a lot of scrutiny, either with genuine intentions, or in an attempt to extort a bribe (don't do that!), or a with combination of both.
Finally, make sure not to overstay in Russia, not even by a few seconds, because Russian laws are notoriously harsh about this. Unlike in many other countries, in Russia it's not possible to simply pay a fine on the spot and board your chosen flight (or otherwise leave the country).