Francisco Albarracin executed a second half try, as Scotland replied from Mark Robertson and Roddy Grant.
BBC: SPORT | Rugby Union | Scottish | Argentina oust Scots from Sevens
Edinburgh, with tries from wingers Tim Visser and Mark Robertson enjoyed a 14-11 interval advantage.
First it was van der Merwe, who interfered with airborne Mark Robertson, in the 21st minute.
Cipriani struck again before Mark Robertson pounced on a diagonal from Phil Godman to bag a home try.
James Eddie and Mark Robertson scored third-quarter tries for Scotland but McFadden and Isaac Boss touchdowns kept Ireland 29-12 ahead.
The Irish visitors were first to score, from stand-off Ian Keatley's penalty, but Rob Moffat's side replied with the first of two Mark Robertson tries.
Kyle Traynor, flanker Alan MacDonald and winger Mark Robertson also came in, while Glasgow were unchanged for the second leg of the annual inter-city contest.
However, the Scottish backs were also getting into their stride and young replacement Mark Robertson finished off a fine move after good work by Nick de Luca.
Visser's counterpart on the other wing, Mark Robertson then ran in a try from his own half, with replacement Phil Godman kicking over all but one conversion.
The Stade Francais number eight is added to Saturday's 22, along with Rob Dewey, Max Evans, Mark Robertson, Nikki Walker, Simon Webster, Kelly Brown, Geoff Cross, Alastair Kellock and Alasdair Strokosch.
Handling in the ruck allowed Paterson to reply from in front of the posts two minutes later as Edinburgh's Ben Cairns was forced off with a head knock, to be replaced by Mark Robertson.
Youngster Euan McLean came in between the sticks in place of the Pole, as Mark Kerr and Jordan Robertson both dropped to the bench.
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