Connecting flights are in the same airport

Hello, my husband and I are interested in visiting Beijing on the 72 hour free transit. We are flying from Bali to Beijing and then from Beijing to Sri Lanka. However, both the arrival and return flights have a layover in Kuala Lumpur, Malaysia. Does this mean we will have to apply for a visa, even if the original and final destination cities are different?

Bali (Denpasar) - Kuala Lumpur - Beijing
Beijing - Kuala Lumpur - Colombo

Kuala Lumpur is just a layover and we will not be staying there.