Sao Tome was cruising on with 1-0 lead until Sri Lanka's Johar Zarwan equalised in the dying minutes to hold them to a 1-1 draw.
The team, which is one point behind table-topper Sri Lanka (4 points), now needs a draw against Macau to qualify for the semifinals.
On the other side, Macau, who lost to Sri Lanka, needs an outright win to make it to the last-four stage.