What education is needed to become a civil pilot?
First, does someone know where I can get my licences for being an civil pilot in Croatia? 


I'm afraid nobody here can help you with that: You will need to find a flight instructor or flight school in your area. (Google can probably help you locate candidate schools, and we have some general advice on selecting a school and selecting an instructor that might help you narrow down your choices.)




  Second, about theoretical knowledge (physics, mathematics), could I watch MIT OpenCourseware on that (and if I do, should I watch this or this? I stumbled upon Flying Academy webiste (can't post the link because I'm new here) and it says "Sufficient level of knowledge of Mathematics and Physics".
  What is sufficient and what would I have to learn?


To begin flight training you don't need to know anything about math or physics: Your initial training will be about manipulating the controls of an aircraft to make it do what you want it to do, and for the moment you don't care how or why it works, you just need to learn the physical technique of controlling an airplane.

At some point in your training you will learn the physics of flight - this is generally part of "Ground School" but your flight instructor may introduce the concepts to you as you approach lessons where they will be relevant.
A basic understanding of the laws of motion and air pressure will be helpful, but everything you need to know can be found in the various FAA handbooks (the Pilot's Handbook of Aeronautical Knowledge, the Aeronautical Information Manual, and the Airplane Flying Handbook are good starting places - regulations will probably differ in Croatia, but the basics of flight will be the same, and are explained in fairly simple language in those books).  

You will also need to be able to work basic flight planning calculations as you advance in your training, which means you will need some basic mathematical knowledge: The ability to add, subtract, multiply, divide, and do simple algebra will cover nearly everything you need to do as a pilot, and higher math is generally not necessary unless you start getting into the Why of aerodynamic theory.