Centre-back Lowe saw red for a nasty foul on Scott Wagstaff with six minutes left as a spirited display by the non-league side ended in misery. For long periods, Halifax, from Blue Square Bet North, tested a much-changed Addicks side but it all went wrong late on.
Charlton finally broke the deadlock in the 40th minute when Paul Hayes burst clear and crossed for Matthew Taylor to rise and send a header looping over Simon Eastwood. Halifax skipper Tom Baker had a stinging effort skim the top of the bar straight after that.
In the second half, the Shaymen served it up to Charlton, but it was only in the 80th minute that the Addicks made victory safe when Johnnie Jackson collected a loose ball in the box and drove into the bottom corner.
Two minutes later, Taylor turned provider when he headed goalwards for Danny Hollands, who controlled well, turned and slotted home from close range.
Halifax lost their heads as Lowe saw red before Charlton wrapped up the scoring in the final minute, Michael Smith crossing from the byline for fellow sub Bradley Pritchard to finish from close in.