The African side had retaken the lead in the 70th minute in what is a crucial Group H fixture for qualification.
However, Senegal couldn't hold on to their advantage and allowed Japan to grab an equaliser just eight minutes later.
The goal came thanks to a terrible misjudgement by the Senegalese goalkeeper. Khadim Ndiaye came for a cross but flapped at it, allowing the Asian side another attempt at an attack.
Substitute Honda controlled the ball which was played back across goal and picked his spot from eight yards to make it 2-2.