Loeb and his hedge fund, Third Point, pressed for Thompson's ouster after a discrepancy about Thompson's education background had been revealed.
The filing, released Monday, was part of a settlement between Yahoo and Third Point, its largest shareholder.
Earlier Monday, The Wall Street Journal reported that Thompson had told directors and colleagues that he had been diagnosed with thyroid cancer days before quitting the post.
It said Thompson disclosed his illness late last week before handing in his resignation, as evidence appeared to emerge that contradicted his claim that he wasn’t responsible for an error in his resume regarding his academic record, sources told the newspaper.
The Journal reported Thompson’s decision to step down as CEO at Yahoo was in part influenced by the diagnosis, which occurred in recent days as the board was investigating why his resume included a computer science degree which he had never attained.
The error in Thompson's resume appeared in a Yahoo regulatory filing and on Yahoo's and other corporate websites.
The struggling Internet company said Sunday that Thompson, its third CEO in three years, would leave immediately and be succeeded by Ross Levinsohn, a senior Yahoo executive who becomes interim CEO.
The Journal reported that Thompson told one colleague that he didn't want to publicly discuss the cancer diagnosis because he wanted to keep personal details private.