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.
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BLADES HARNESS THEIR EMOTIONS
CHRIS Wilder reflected on an emotional afternoon which saw tributes paid to former player George Baldock, who passed away earlier this month, as his Sheffield United side beat Stoke City.
DRAGONS HAVE PLENTY OF PUFF!
Dan has faith in squad...
McCANN HAILS HIS ROVERS AS HERO HURST STEALS SHOW
GRAHAM McCann called Kyle Hurst âa joy to watchâ after his Doncaster Rovers sideâs victory at Valley Parade.
MATT'S FINISH EARNS POINT IN LAST-GASP PEN DRAM
CHARLTON boss Nathan Jones broke his habit of not watching penalties as Matty Godden converted in the 97th-minute to salvage a draw against Wrexham.
TON-UP CARRICK BOYS TO KEEP
AT CARROW Road this afternoon, Michael Carrick will take charge of his 101st game as Middlesbrough manager.
THREE MOORE POINTS -JUST
PORT VALE manager Darren Moore praised the âmentality changeâ from the clubâs supporters as his side held on to beat AFC Wimbledon and extend their lead at the top of the League Two table.
SUPER SUBS HELP COOK TURN UP HEAT
CHESTERFIELD boss Paul Cook said the strength of his squad was the difference as three of his substitutes scored second-half goals against struggling Morecambe.
SKY BLUES' LATE RALLY HAS MARK 'HUMBLED'
MARK Robins claimed his Coventry team were thoroughly deserved winners after his side completed a spectacular comeback to win against ten-man Luton Town.
CASPER HAUNTS THE SWANS ONCE AGAIN
CASPER De Norre struck a dramatic 90th-minute winner for Millwall as Swanseaâs Championship goal drought continued.
Eustace's rage over penalty winner
BLACKBURN boss John Eustace blasted referee Darren England for a âdisappointingâ penalty decision which handed Watford a narrow victory.