The Gills were beaten by the odd goal in three by Hearts in a physical work-out at Priestfield Stadium on Thursday evening.
Luke Rooney put the Gills ahead with a 49^th minute penalty before the Scottish Premier League side hit back to win.
Gillingham boss Andy Hessenthaler went with a 4-5-1 formation, Stefan Payne being the main target man. Two of the other summer signings, Tony Sinclair and Danny Spiller, were at right-back and on the right-side of midfield respectively.
In the fifth minute Chris Palmer curled in a free-kick from the right and Stefan Payne forced keeper Janos Balogh, in a luminous yellow kit, into a juggling save.
A great crossfield ball from Palmer sent Andy Barcham down the right, he went past Lee Wallace and cut into the area. The Gillingham winger seemed to be clipped from behind by the Hearts left-back and went down but referee Gavin Ward, who was well placed, waved away the penalty appeals.
Hearts backed by a healthy number of vociferous travelling fans in the Gordon Road stand took a while to settle but gradually began to increase the pressure on the Gills rearguard.
Curtis Weston won a challenge in midfield and Palmer broke forward, although he had options, the in-form midfielder struck a fierce shot goalwards which the Hungarian keeper was happy to watch whistle inches over.
The Gills went close to taking a 25^th minute lead thanks to the Jambos Adrian Mrowiec. A neat build-up involving Spiller, Barcham and Stefan Payne saw Polish midfielder knock the ball towards his own net but Darren Barr was in the right place to clear off the line.
Calum Elliot created the Edinburgh sides first real threat in the 35^th minute with a strong run into the box but his weak shot was saved by Alan Julian.
Almost immediately at the other end Weston stole the ball from Eggert Jonsson and his long range strike forced Balogh into a full length save low to his right.
The Gills were gifted the opportunity to take a 49^th minute lead when Ismael Bouzid clumsily felled Payne in the area. This time the referee pointed to the spot and half-time substitute Luke Rooney smashed home the resultant penalty high past Balogh.
Unfortunately the lead lasted less than two minutes. The Gillingham defence was split by Ryan Stevenson's inch perfect pass and Arvydas Novikovas finished clinically with a low finish past Julian.
In a good period for the visitors Lithuanian youngster Novikovas curled a free-kick inches over and moments later Elliot's fierce shot forced Julian into a flying save after Jonsson won a challenge with the Gills other substitute at the break Kevin Maher.
The Gills responded with hopeful shots from distance by Maher and Rooney but both dragged their efforts wise before Danny Jackman, Stanley Aborah and strike duo Adebayo Akinfenwa, signed earlier in the day from Northampton, and Mark McCammon were introduced.
A Craig Thomson pass from deep found Stevenson out on the left, his back heel fed David Templeton who saw his shot fly across the face of goal.
Then in the 84^th minute the Scottish Premier League side took the lead, Templeton's corner from the left was powerfully headed home by Algerian Bouzid. Soon after left-back Lee Wallace went close, he fired in a low angled drive straight at Lance Cronin.
Jim Jeffries team now move on to play Millwall in a testimonial game for ex-Gill Neil Harris at the New Den on Saturday.