DesiredCapabilities dcaps = new DesiredCapabilities();
String[] phantomArgs = new  String[] {
        "--webdriver-loglevel=NONE"};
dcaps.setCapability(CapabilityType.ACCEPT_SSL_CERTS, true);
dcaps.setCapability(CapabilityType.SUPPORTS_ALERTS, true);
dcaps.setCapability(PhantomJSDriverService.PHANTOMJS_EXECUTABLE_PATH_PROPERTY,
        phantomjs.getAbsolutePath());
dcaps.setCapability(PhantomJSDriverService.PHANTOMJS_CLI_ARGS, phantomArgs);
dcaps.setJavascriptEnabled(true);
WebDriver driver = new PhantomJSDriver(dcaps);

JavascriptExecutor js=(JavascriptExecutor) driver;
String script = "window.confirm = function(message) {"+
        "document.lastConfirmationMessage = message; return true; }";
js.executeScript(script);
driver.get("http://www.mysiteWithConfirm.de");
Object message = js.executeScript("return document.lastConfirmationMessage");