AFL ticket agency Ticketek will refund the handling and service fee to AFL, Adelaide and Sydney members after long delays on Tuesday morning.
Fans were left frustrated when trying to buy tickets for Saturday night's semi-final between the two sides at the SCG.
The glitch also applied to tickets for Friday's other semi-final between Hawthorn and the Western Bulldogs.
While the agency insisted the website kept functioning, fans faced delays and site time-outs.
"The AFL was extremely disappointed for our fans today, and made this clear to Ticketek," said AFL chief executive Gillon McLachlan.
"I personally spoke to Ticketek, the SCG and the MCG to express the frustration of our fans.
"The decision to refund the service and handling fees on every transaction from tickets sold today to AFL, Crows and Sydney members is a good gesture from Ticketek this afternoon."