The deal was thrown into doubt after Yahoo was twiced hit by cyber attacks, with the original enterprise value of the agreement eventually dropped by US$350 million in an effort to push it through.
She will take a compensation package presently worth around $127 million that includes severance pay and stock awards which will be fully conferred with the completion of deal.
In an email to employees that Mayer posted on Tumblr, she wrote, "Given the inherent changes to my role, I'll be leaving the company".
While the acquisition deal was announced in July last year, the process has been delayed as the companies had to deal with the aftermath of two data breaches suffered by Yahoo! last year.
About 2,000 Yahoo and AOL workers are expected to lose their jobs as Verizon trims expenses and eliminates overlapping positions. He will now be the CEO of a new Verizon subsidiary- Oath, which will comprise of Yahoo and various AOL services.
There was also the blink-and-you-missed-it tenure of Scott Thompson, a former PayPal executive who lasted only a few months as CEO at Yahoo in early 2012 before it was revealed that he had numerous discrepancies on his résumé.
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Mayer went on to say that Yahoo has "confronted seemingly insurmountable business challenges, along with many surprise twists and turns" during her tenure.
Verizon will compete with Facebook and Google for online advertising.
"We're creating the future of brands by utilising powerful technology, differentiated data and trusted content". She added that the range of assets across Verizon and Oath, from VR, AI and 5G to IoT and content partnerships will "create exciting new ways to captivate audiences across the globe". "We have been dominating the customer brands in news, finance, sports, tech, lifestyle and entertainment, along with our market leading platforms for advertising technology", he said.
The Yahoo name is going to disappear and the company is going to be approapriately called Oath.
Yahoo's stake in the e-commerce giant, Alibaba, and Yahoo Japan will be diverted into a holding company called Altaba, Inc.