After being outplayed for most of the first half, Reading turned the tables on unlucky Gillingham to snatch a late winner and give new manager Steve Coppell a victory in his first match in charge.
Gillingham could have been ahead after just 45 seconds but Rod Wallace saw his effort hit the Reading upright and bounce clear.
"We can't use the word 'unlucky' because we have banned it from the dressing room," said Gillingham coach Wayne Jones.
Wallace was not the only Gillingham player to miss in a lively first half with Marlon King firing over the bar when he should have done better.
Coppell's half-time team talk seemed to have done the business as the Royals took the lead nine minutes into the second half.
Full-back Nicky Shorey slung a high cross from the left wing to the far post where Scott Murray jumped highest to head across the face of goal and inside the far post.
Gillingham, and King in particular, missed several chances before their equaliser finally arrived thanks to a mistake by Reading keeper Marcus Hahnemann. He completely miskicked a clearance leaving King with the simple task of putting the ball into an empty net.
A draw was probably a fair result but Reading were not finished. Five minutes before the end, a three-man move saw Shaun Goater tee up a shot for Steve Sidwell.
From fully 20 yards out, the England Under-21 midfielder cracked home Reading's winner.
"I am pleased with the result, but I know we can play better than that," said Coppell.
"It was the unquantifiable characteristics of resilience and team unity that brought about that result.
"I can't take much credit for the result personally, because I have only had one full training session with the whole squad since my appointment."