The company also voluntarily paid $122,174 to TradeMe trust which has since been passed on to each of the 110 victims.
Defence counsel for The Auto Co, Donald Webster, said in his written submission that when Mr Umeoka was made aware of the behavior, he immediately sought legal advice to understand what had been done wrong and now fully understands the nature of the offending.
"The initial interview with the defendant's director made it clear that the defendant's director did not realise that it's actions were illegal," Mr Webster said.
"The practice is apparently rife in Japan, where the defendant's director comes from and it was not understood that it was illegal in New Zealand."
Judge Ajit Singh reduced the original sentence by almost half, giving the company credits for its co-operation, change in systems since the shill bidding was uncovered, the personal circumstances of Mr Umeoka that the company had already paid reparations.
He sentenced the company to pay a total of $42,000 for all 13 charges.
Trade Me head of trust and safety Jon Duffy said he was pleased to see the fine imposed.
"It's a good result, but on behalf of the Trade Me members ripped off along the way, we'd have liked the court to have issued a fine closer to the maximum which is $200,000."
Mr Duffy said shill bidding was "a blight" that sucked the oxygen out of an auction marketplace.
"Intentionally inflating the sale price via fake bidders is dishonest, and it undermines the trust of our community and the integrity of our website.
The company was the biggest motor trader on the site at the time and the case is the largest of its kind in New Zealand.