A late Danny O'Callaghan header gave the visiting Scholars the three points as he met a 90th minute corner.
In strong, swirling winds and heavy rain,. Chasetown survived Yaxley hitting the crossbar and Luke Yates winning a strong tackle to deny a counter attack.
Chasetown hit the post themselves and the introduction of Joe Morley and Danny O'Callaghan asserted the almost constant second half pressure.
3 floodlights going out for around 10 minutes and a lack of footballs almost saw a bizarre end to a game that Chasetown deserved to win.