Commissioner Anna Rawlings said overcharging customers - even small amounts - can result in hefty fines for companies.
"Spark failed to take necessary steps to ensure its invoices were accurate," Rawlings said.
"Customers rely on companies to invoice them accurately. Overcharging even a small amount to individual customers can result in businesses receiving large sums of money that they are not entitled to."
More than 7000 Spark customers still remained out of pocket despite refunds being made by the company, Rawlings said.
In sentencing, Auckland District Court Judge Russell Collins said: "Commercial offending must be met with commercial penalties."
Separately, the commission has issued Spark with a warning relating to its failure to correctly apply a $300 welcome credit to certain accounts.
In a statement, Spark said it sincerely regretted the impact on the customers and had refunded those who were incorrectly billed or did not receive the welcome credit as advertised.
"Spark has fully co-operated with the Commerce Commission during this process, which resulted from mistakes with no malicious intent," a spokesperson said in the statement.
"Spark sincerely regrets the impact on customers and has taken all practicable steps to refund those customers who were billed incorrectly or did not receive their welcome credit."
The company said the Court took into account Spark's conduct during the Commerce Commission investigation, and entering into a guilty plea, when it determined the financial penalty.
"Spark has fully refunded existing customers and the vast majority of former customers, and has sent a letter or email to the last known address of former customers with a credit balance of $1 or more."
It advised that the fine would not impact Spark's FY19 guidance.
Rawlings said it was vital businesses clearly disclosed the terms of any offers made when marketing their products.
"This is another example of the care businesses must take to ensure their billing and invoicing systems are accurate and that customers are not left out of pocket," she said.
"We encourage all businesses to regularly review their systems and processes to ensure that their products and promotional offers are being delivered to their customers as intended."