Kemi Adeosun, who lived in the UK until she was 34, said she had been told she was exempt because she was over 30.
The former investment banker said she was issued with a certificate that she thought was genuine.
But an internal investigation showed that it was forged.
Ms Adeosun’s resignation follows months of speculation in local media about whether her National Youth Service Corps certificate was genuine.
The dual Nigerian and British national did not initially comment on the claims, leading to criticism from her opponents.
However, in a statement, she said she felt bound to resign after the investigation result became known.
“This has come as a shock to me and I believe that in line with this administration’s focus on integrity, I must do the honourable thing and resign,” she said.
Ms Adeosun was appointed as finance minister by President Muhammadu Buhari in 2015. Her main policy was a bid to improve tax collection and crack down on mismanagement by government agencies.
The minister of state for budget and national planning, Zainab Ahmed, will oversee the finance ministry with immediate effect, the presidency said.
Nigerian university students have to do a year of national service upon graduation as a way of ensuring that graduates contributed to Nigeria’s development.
“I [thank] you profusely for the honour & privilege of serving under your inspirational leadership. It‘s been a truly rewarding experience to learn from you & to observe at close quarters your integrity & sense of duty.” Full Text of my Resignation Letter: https://www.facebook.com/410055792680404/posts/701058226913491/ …
Corp members are posted to states outside their state of origin to encourage national unity.
Nigerian graduates are not eligible for government work or many private jobs until they have completed the mandatory year of service.