I am a Malaysian passport holder travelling to Tokyo transiting through Shanghai Pudong Airport.

If your layover is less than 24 hours, you are definitely covered by 24 hour visa free transit and you do not need any kind of visa. If you want to exit the airport that is another detail and to do that, you will approach 24/144 hour visa free transit counter where you will apply for a temporary entry permit. This permit is granted based entirely on discretionary right of the airport authorities on a day and you can expect both outcomes, positive and/or negative. The exit outside the airport is not a passenger right, but more something like bonus. If you intend to spend a night in Shanghai, you will be definitely asked to present an accommodation booking confirmation, so I strongly suggest you to have your booking printed out and at hand. This application for a temporary entry permit is free of charge.

The 144 hours visa free only apply to 53 countries which it does not includes Malaysia right?

You are correct, but here we had an example of 24 hour visa free transit and Malaysian citizens are perfectly eligible to use this option. Hopefully even 144 hour visa free transit will be extended to some other countries in the foreseeable future, Malaysia included.