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.

Phillips, part of Wales' squad for the November Tests, suffered the injury in Scarlets' loss to Ospreys on Saturday.
The 27-year-old, capped three times, was on the bench in Wales' historic victory against South Africa.
But Scarlets scrum-half Gareth Davies is fit again after a knee injury.
Once-capped Davies could face Ospreys in the Pro12 on Saturday after playing in Llanelli RFC's 58-21 Welsh Premiership win over Bridgend last weekend.
Davies was injured in Scarlets' 26-13 Pro12 win over Newport Gwent Dragons on Sunday, 5 October, ruling him out of Wales' November Tests.
The 24-year-old made his Wales debut as a replacement on their June, 2014 tour to South Africa having shone for the west Wales region last season.
Wales begin their Six Nations campaign at home to England on Friday, 6 February, before ending the tournament away to Italy on Saturday, 21 March.
Phillips was an unused replacement against the Springboks and Fiji during the autumn campaign and won his last international cap against Tonga in November 2013.
He will undergo surgery on his right shoulder on Friday, 2 January after being replaced just before full-time in the 17-15 defeat at the Liberty Stadium.
Fellow Scarlets hooker Ken Owens, who deputised for then-injured Richard Hibbard in South Africa, is also yet to return after undergoing neck surgery in September.
"Ken's still a few weeks away - we're not putting a deadline on that," said Scarlets head coach Wayne Pivac.
Gloucester's Hibbard was unable to play in Wales' November win against the Springboks because the game was played outside World Rugby's Test window.
That gave Ospreys hooker Scott Baldwin the chance to play in the 12-6 win.
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.
[NEXT_CONCEPT]
Scarlets hooker Emyr Phillips is likely to miss Wales' Six Nations campaign as he prepares to undergo surgery on a dislocated shoulder, which will sideline him for up to 12 weeks.