I created a timer using Javascript,But in that i used system time.
If that JavaScript really serves your needs, then that JavaScript code could easily be made dynamic as well. In the code, wherever the current system time is initialized, simply insert your server time using your language of choice (Python). In other words: use your server language (Python) to output the script just as it is right now, except for replacing the part that initializes the current time.
In PHP, some pseudocode (not sure about the arguments of the Date() constructor) might look like, for example:
// my_countdown_script.php
[..]
var startTime = new Date( <?php echo time(); ?> );
[..]
Then, rather than including your JavaScript, you would be including the PHP file that inserts the server time like above:
<script type="text/javascript" src="my_countdown_script.php"></script>
The good thing is: this will work in any browser that supports the JavaScript you already created.
(In some later version, your JavaScript could include some initializers that allow you to set the current time after including the library in your HTML. That would allow the actual JavaScript library to be static, and thus to be cached by the browser.)