The Gills, who were top earlier this month, suffered their third straight defeat at Priestfield as Dara Costelloe's goal in time added on stole the points for the visitors.
Earlier, Armani Little had broken the deadlock for the hosts before Ben Woods levelled on the hour.
Gillingham looked the most likely to win it before Burnley loanee Costelloe's fourth goal in three games stole the spoils right at the very end.
Bonner groaned: "We are as angry and frustrated as you could imagine we would be at losing late, but probably the team that was going to win it was them.
"We gave them too many chances in the second half, it was way too easy to create a chance against us. The second goal is a disgrace from us.
"It's a disgrace. It's a free-kick, deep in the pitch, and we don't head it.
And then we're so easy to work through.
This story is from the October 13, 2024 edition of The Football League Paper.
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This story is from the October 13, 2024 edition of The Football League Paper.
Start your 7-day Magzter GOLD free trial to access thousands of curated premium stories, and 9,000+ magazines and newspapers.
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