Hell Pizza responded by removing the original Facebook post and replacing it with a message explaining it thought the winning entry was "in the spirit of a prank between mates".
It offered to donate $10,000 to Wellington Rape Crisis, which has been forced to cut its services by 20 per cent because of a funding crisis which has left a $55,000 shortfall in its 2012/13 budget.
The company would also match every donation made at the agency's fundraising page dollar for dollar until the end of the month.
Wellington Rape Crisis manager Natalie Gousmett this afternoon confirmed her organisation was accepting the offer on the condition Hell senior executives, managers and staff going through sexual violence awareness and ethical bystander training run by her agency.
Ms Gousmett said she was disappointed at having to accept the donation, rather than relying on guaranteed funding.
"They've made a mistake in a way that treats sexual violence as a joke. I feel as an agency that works with survivors of sexual violence it's really troubling for us to be in this position of having to decide whether to have to accept money from a person who's done something like this when we should have consistent Government funding."
In a post on Facebook, Hell blamed a social media manager for its original post.
It said the post was not approved by Hell owners and co-founders Callum Davies or Stu McMullin.
"We unreservedly apologise for this comment and have taken steps to stop it from reoccurring. Sexual assault is no joke and we would like to use the massive level of discussion on this to highlight the need of Wellington Rape Crisis."
Wellington Rape Crisis has been providing support services to rape victims for 35 years.
It faced funding problems after its client list grew from 543 in 2010/11 to 995 in 2011/12.
It's not the first time Hell Pizza has apologised for its marketing decisions.
The company said sorry after including the message "You will marry a transgender" in its "misfortune" cookies last December.
In 2011, Hell was accused of "spiritual abuse" for putting up a billboard showing a bun decorated with an inverted pentacle symbol and the words: "For a limited time. A bit like Jesus."
A 2006 campaign where condoms were randomly mailed out prompted a record 685 complaints to the Advertising Standards Authority. The complaints were upheld.