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I have a button
<input type="submit" value="Click Me" onclick="substitute()"/>
In one of my first HTML5 pages. Is there anyway I can write the body of the substitute method in C# code?
Or is it that I have no other option other than JavaScript?
The only way to have C# respond to a web page is to POST the page to a web server, or execute an AJAX request. On the web server side, your request will execute some method that contains C# code.
But it really depends on what you are trying to do; some things are better handled in the browser. Study up on ASP.NET MVC and Javascript, and your strategy will become clearer.