She had made about $600 before tax working 50 hours a week, so she would have qualified for the maximum paid leave rate of $488.17 a week for 14 weeks, or $6834.
Human Rights Commission spokeswoman Christine Ammunson said it was illegal to refuse to employ someone because of pregnancy.
But Triangle Service Station co-owner Bill Carson said the company chose staff based on what he called "the Z factor - how they interact with our customers and their workmates and how they do their job".
"We make our employment decisions based on the 'Z factor' and best fit for the role, and do not discriminate based on gender, ethnicity or any other factor," he said.
Ms Thompson has two other children aged 5 and 2. They all live with Ms Thompson's mother and brother and the brother's son in a three-bedroom state house across Kupe St from the petrol station.
Ms Thompson's partner does not live with them but helps out financially, so she does not qualify for a welfare benefit.
That means her sole income is now family tax credits and child support totalling $217 a week. She pays her mother $150 a week in rent.
"Early last year, Work and Income wrote a letter saying 'you have to go and look for employment now that your son is turning 5'," she said.
"That's what I did. My daughter is in kohanga reo and I have a good relationship with my childcare centre and they were very keen to take the baby so I could go back to work after 14 weeks. I really wanted to go back to work."
Paid parental leave
*Fourteen weeks, which can start up to six weeks before due date if arranged with employer in advance.
*Pays a woman's full pay or $488.17 a week, whichever is lower.
*Woman must have worked for the same employer for at least 10 hours a week, and at least one hour in every week or 40 hours in every month, in the six or 12 months immediately before baby's due date.
Read more
For more on Pregnancy and birth click here.