72 hours including layover?

Hello. I am a UK citizen travelling from Jakarta into Beijing, then from Beijing on to Tokyo. I am planning on spending some time in Beijing under the 72hr visa waiver, but the flight on to Tokyo has a 9hr layover in Shanghai which would take me over the 72 hours. Do I need to book an earlier flight to compensate for this or is my time of leaving taken from when my flight leaves Beijing? (I don't plan on leaving the airport in Shanghai by the way!). Thanks