After searching for few hours, I ended up having the following, and it worked well. Hope this helps someone else in future.
HTML and JS code: loging.html:
<html>
 <head>
    <title>Flask Intro - login page</title>
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <link href="static/bootstrap.min.css" rel="stylesheet" media="screen">
    <script type="text/javascript" src="http://code.jquery.com/jquery 2.1.4.min.js"></script>  
 </head>
 <body>
    <input id="submitbutton" type="submit" value="Test Send Data">
    <!----------------------------------->
    <script type="text/javascript">
    function runPyScript(input){
        var jqXHR = $.ajax({
            type: "POST",
            url: "/login",
            async: false,
            data: { mydata: input }
        });
        return jqXHR.responseText;
    }
    $('#submitbutton').click(function(){
        datatosend = 'this is my matrix';
        result = runPyScript(datatosend);
        console.log('Got back ' + result);
    });
</script>
Python code: app.py:
from flask import Flask, render_template, redirect, url_for,request
from flask import make_response
app = Flask(__name__)
@app.route("/")
def home():
    return "hi"
@app.route("/index")
@app.route('/login', methods=['GET', 'POST'])
def login():
   message = None
   if request.method == 'POST':
        datafromjs = request.form['mydata']
        result = "return this"
        resp = make_response('{"response": '+result+'}')
        resp.headers['Content-Type'] = "application/json"
        return resp
        return render_template('login.html', message='')
if __name__ == "__main__":
    app.run(debug = True)