Sao Tome, which played a more aggressive game and had better share of exchanges, took the lead in the 29th minute through Gastao Patricio Souza Basto.
Sri Lanka put up a better performance in the second-half and equalised in the 90th minute through substitute Johar M Zarwan.
Sri Lanka finished their league engagements in Group A with four points. Sao Tome and Principe now need a draw against Macau to advance to the semis as the second-best team from Group A.