The late flurry was out of context with the rest of the match as Wolves struggled to get into gear and found themselves trailing to a Darius Henderson strike after 55 minutes.
That was the first goal Gillingham had scored in 352 minutes of action.
But Kenny Miller cancelled out that strike when he dragged Wolves back on to level terms with his 13th goal of the season just five minutes later.
A point was of little use to either side as Wolves badly needed a win to kick-start their slim play-off hopes while Gillingham were just as desperate for a victory to boost their survival hopes.
Wolves almost paid the price for a sluggish start when only the woodwork prevented Gillingham taking a 29th minute lead.
Lee Naylor fouled Matthew Jarvis and from the resulting free-kick, Nicky Southall beat goalkeeper Michael Oakes only to see the ball bounce to safety off the bar.
Coming so close to falling behind finally sparked Wolves into life and they enjoyed their best spell of the half in the final ten minutes.
But they could not find a way past Gillingham goalkeeper Steve Banks who saved well from Lee Naylor, Seyi Olofinjana and Carl Cort.
They proved to be vital saves by Banks as Gillingham stunned Molineux ten minutes into the second-half when Henderson struck.
Jody Craddock failed to cut out a cross by Darren Byfield and Henderson was on hand to steer home his sixth goal in his last 26 appearances for Gillingham.
But, just as in the first-half when Wolves were rocked by Southall's free-kick, they stepped up a gear after falling behind and were rewarded in the 60th minute.
Rob Edwards floated a hopeful looking right wing cross into the area but the alert Scottish international Miller was on hand to poke a header past Banks from eight yards, for his third goal in four games.
The game looked set to meander to a 1-1 draw but Flynn, a recent capture from Wigan, sparked the late flurry of action when he raced on to a long clearance from Banks and lifted the ball over Oakes.
It looked good enough to pull off a shock double for the Gills but Clarke was on hand to spare Wolves' blushes.
A hopeful cross into the Gillingham area led to confusion between defenders Ian Cox and Nyron Nosworthy and Clarke stabbed the loose ball home.