I am trying to execute javascript on a page when I click on a button in popup.html. I tried to use such a way:
In background.js:
chrome.tabs.onUpdated.addListener(function(tabId, changeInfo){
    if(changeInfo.status == "loading") {
        insert(tabId);
    }
});
function insert(tabId) {
    chrome.tabs.get(tabId, function(tab) {
        $('button').click(function() {
            chrome.tabs.executeScript(tab.id, {file: 'js/alert.js'});
        });
    });
}
Alert.js consists only of one string: alert('works');
Alert is just an example. Real script should do some DOM manipulation with opened tab after user clicks on a button im popup.html.
I wrote a demo for your need.
https://gist.github.com/greatghoul/8120275
alert.js
alert('hello ' + document.location.href);
background.js
// empty file, but needed
icon.png

manifest.json
{
  "manifest_version": 2,
  "name": "Click to execute",
  "description": "Execute script after click in popup.html (chrome extension) http://stackoverflow.com/questions/20764517/execute-script-after-click-in-popup-html-chrome-extension.",
  "version": "1.0",
  "icons": {
    "48": "icon.png"
  },
  "permissions": [
    "tabs", "<all_urls>"
  ],
  "browser_action": {
    "default_icon": "icon.png",
    "default_popup": "popup.html"
  },
  "background": {
    "scripts": ["background.js"],
    "persistent": false
  }
}
popup.html
<!DOCTYPE html>
<html>
  <body style="width: 300px">
    Open <a href="http://stackoverflow.com" target="_blank">this page</a> and then 
    <button id="clickme">click me</button>
    <script type="text/javascript" src="popup.js"></script>
  </body>
</html>
popup.js
// var app = chrome.runtime.getBackgroundPage();
function hello() {
  chrome.tabs.executeScript({
    file: 'alert.js'
  }); 
}
document.getElementById('clickme').addEventListener('click', hello);
                        You can also use Messaging:
in popup.js
document.getElementById("clicked-btn").addEventListener("click", function(e) {
    chrome.runtime.sendMessage({'myPopupIsOpen': true});
});
in background.js
chrome.runtime.onMessage.addListener(function(message, sender) {
      if(!message.myPopupIsOpen) return;
      // Do your stuff
});
Not tested but should works, further informations about Messaging.
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