First Minister Nicola Sturgeon described the case as "shocking" after Moray SNP MSP Richard Lochhead raised the issue earlier this month.
He said rural constituents were being "fleeced" with such charges.
Halfords said the fee was exceptional for an online exclusive product but that a £2.99 fee would now be charged.
Halfords said in a statement: "When ordering from Halfords.com, normal carriage costs to the Highlands and Islands region apply in over 95% of cases.
"The exception to this was if a customer purchased an online-only exclusive product on Halfords Marketplace which is an online platform that Halfords hosts for smaller independent retailers who deliver direct.
"We agree that the previous charge did not make sense if a Marketplace customer was ordering one item at a small cost and having completed a review, we have reduced the carriage costs to a standard £2.99.
"All suppliers have been notified. Halfords will subsidise the difference whenever the carriage cost is more. We would like to apologise for the frustration this charge has caused for our Marketplace customers."
Moray SNP MP Angus Robertson had initially written directly to Halfords chief executive Jill McDonald.
He said: "Halfords' decision to quickly review and change their delivery charges policy so that a flat rate now applies regardless of where the customer lives is a very welcome change of heart.
"This action by Halfords demonstrates how important it is to challenge companies large and small on their delivery policies to areas like Moray and the Highlands."
Welcoming the news, Mr Lochhead said: "Excessive delivery charges are a massive frustration for people in Moray and across Scotland.
"Halfords decision to now apply the same charge across the board is to be welcomed and I want to see other companies following this example.
"There are many delivery options available to companies, including Royal Mail and there is simply no excuse for companies to discriminate against consumers in Scotland.
"Until companies stop treating customers in rural Scotland with contempt when it comes to delivery charges then we will continue to take a hard line on naming and shaming them."
A study by the Citizens Advice Bureau in 2015 found consumers in the Highlands and islands were paying substantially more for delivery charges.
Halfords has revised delivery charges for the north of Scotland after a £50 delivery charge to send towels costing £5.99 to Speyside was criticised.