Found in 2 comments on Hacker News
duskwuff · 2017-08-25 · Original thread
Not an online course, but my go-to recommendation is "FPGA Prototyping by Verilog Examples" [1]. Or, if you want to learn VHDL, [2].

[1]: https://www.amazon.com/dp/0470185325

[2]: https://www.amazon.com/dp/0470185317

sabot · 2015-01-02 · Original thread
It's half of your question, but a good basic electronic logic simulator is http://www.cburch.com/logisim/

A digital electronics book could be paired with it for exercises. Or heck build your own microcontroller or something.

A similar method is to instead of using a game to simulate circuits in software, use an FPGA to simulate a circuit in hardware. A cool book I've used to here, http://www.amazon.com/FPGA-Prototyping-VHDL-Examples-Spartan...

It will take you step by step from creating simple shift registers to displaying an image over VGA (which you implement yourself).