England won the toss at the Grange for the first meeting at this level between the neighbours with the inclement conditions restricting play to 44 overs a side as persistent rain spoilt the contest.
England fielded debutant Samit Patel and recalled Flintoff - after nearly a year on the ODI sidelines - as well as Matt Prior and Tim Bresnan.
Flintoff and company would have embarrassed their hosts had it not been for a solid knock of 60 off 119 balls by former Yorkshire all-rounder Gavin Hamilton, who bagged three sixes and put on 64 for the fourth wicket alongside policeman Colin Smith.
It was a far cry from Hamilton's sole England Test against South Africa in Johannesburg nine years ago, when 15 overs brought no bowling return and he produced a pair of ducks.
Nottinghamshire all-rounder and left-arm spinner Patel, preferred to Graeme Swann, made an early breakthrough with a runout of opener Ryan Watson for 1.
Yorkshire all-rounder Bresnan then claimed the wicket of Durham batsman Kyle Coetzer, one of four members of the Scotland line-up with county experience, for a duck.
Discarded after poor form two years ago in a series against Sri Lanka, Bresnan only the squad after injuries to Ryan Sidebottom and Chris Tremlett but forced Coetzer to edge too close to Flintoff at second slip.
Bresnan next removed Warwickshire's Nav Poonia, who edged to Patel at third slip before the Scots survived for another 20 overs without further loss.
Hamilton enjoyed a reprieve on 24 when James Anderson fumbled a chance at second slip and then Owais Shah missed the rebound.
Hamilton escaped again when he drove at Stuart Broad and this time Luke Wright missed the catch.
The partnership was finally broken when Smith, who had battled to 36 off 67 balls including three fours and two sixes, upper cut Broad and was caught at third man by Alastair Cook, a substitute fielder for Flintoff during a brief absence from the field.
There was more joy for Patel as new batsman Neil McCallum slogged straight to Anderson in the deep.
Six overs after the re-start following a rain break, Broad bowled Craig Wright off an inside edge.
Hamilton's resistance was finally broken when he was superbly caught by Prior attempting to guide Flintoff to the third man boundary.Flintoff claimed two more wickets in successive deliveries in the final over to finish with figures of three for 21 to leave England a modest target but with the score on 10 for no wicket a third heavy shower killed off the action, an Ian Bell boundary the sole highlight.
On Wednesday, England, just five wins in their last 15 one-day internationals, face South Africa at Chester-le-Street in a Twenty20 International.