Thompson scored the only goal of the game against the play-off chasing 'Addicks' providing a fairtale end to an incredible story.
The 29-year-old was first diagnosed with Hodgkin Lymphoma in 2013 during his time with Tranmere, but was given the all-clear the following year.
However, the cancer returned in March 2017, only for Thompson to once again return to action in December after being given the all-clear.
The goal was Thompson's first since he got back playing and he believed there was just the slightest hint of divine intervention.
"You can say it's written in the stars, fate, destiny and there's been a lot of hard work I've had to do," he told 'BBC Radio Manchester'.
"It's all come down to today and it's proven that it's been worth it."
The goal, coupled with Oldham and Northampton playing out a draw saw the 'Dale' avoid relegation and Thompson could scarcely have been more pleased.
"It's been a rollercoaster but today's a massive high, a massive, big moment for my family and I'm sure we'll celebrate and enjoy it."