The Blues had held a slim half time lead thanks to skipper Xavier Rush's try.
Ben Blair and Patterson swapped penalties at a sparse Murrayfield, before Rush went over for the game's opening try.
Edinburgh did well to halt an initial drive from a five metre line out, but allowed their defence to be sucked to the open-side as Nick Robinson switched the play back right.
The fly-half's pass dipped short and bounced off a Blues knee, but Rush gathered coolly to dive over for an unconverted try.
Despite attempts to be positive, the game became bogged down in the middle of the park as both sides searched for that extra bit of inspiration to break through watchful defences.
Patterson looked as likely as anyone with his eye for a gap and quick feet, but even he had to settle for a second penalty kick after Blues flanker Rhys Shellard was pinged for hands in the ruck.
Still holding on to an 8-6 lead, the Blues did put one flowing move together just before half-time that ripped through the Scots, only for a fine last ditch tackle to deny Marc Stcherbina.
Blair stretched the visitors' lead after the break with a long-range penalty that bounced over off the crossbar. But Shellard earned 10 minutes in the sin-bin, after being caught one time too many slowing down possession and Edinburgh soon took advantage.
Kicking for the corner, the Edinburgh pack caught and drove, shunting the Blues backwards and carving out the gap for hooker Kelly to barge over.
Patterson's conversion gave Edinburgh a 13-11 lead, although the Blues should have hit back straight away only for replacement James to spill the ball with the line at his mercy.
The Scots seemed to be heading for four points, but two minutes into injury time had the victory ripped away. The Blues broke through into the Edinburgh 22, before spinning the ball left quickly for replacement White to go over, Blair converting superbly.
Still reeling from that blow, Edinburgh had even the small consolation of a losing bonus point taken away as James made amends for his earlier blunder by racing in at the corner.
To complete a miserable night for Edinburgh, Scotland back-row Ally Hogg suffered a fresh injury scare just a week before their autumn Test series. Hogg came off the Edinburgh bench midway through the second half, with the aim of proving his fitness to Scotland coach Frank Hadden following a month on the casualty list. But after only six minutes Hogg hobbled off in pain after suffering a fresh knee problem.
Edinburgh: C Paterson, (capt); M Pyke, B Cairns, P Jorgensen, D McCall; D Hodge, G Laidlaw; A Jacobsen, A Kelly, C Smith, M Mustchin, S Turnbull, A Strokosch, R Rennie, D Callam
Replacements: S Lawrie, A Dickinson for Smith (49), D Hewett, F Pringle for Hogg (62), A Monro, A Hogg for Rennie (47), S Webster for Jorgensen (70)
Blues: B Blair; M Luveitasau, J Robinson, M Stcherbina, C Czekaj; N Robinson, E Fairhurst; J Yapp,G Williams, T Filise, D Jones, J Goode, S Morgan, R Shellard, X Rush (capt)
Replacements: S Roberts for G. Williams (65), D Goodfield, B Davies for Morgan (68), B White for Shellard (62), W Evans for Fairhurst (62), N Macleod for J. Robinson (80), T James for Luveitasau (65)
Referee: George Clancy (RFU)