A last gasp goal was enough to send Boro to their second defeat in their pre-season programme.
Luke Young played his first game in a Boro shirt, following his midweek move from Charlton.
The team for the game in Edinburgh on Saturday was:
Jones, Young (Hines 61), Taylor, Davies, Wheater, Boateng (Kennedy 87), Arca, Morrison (Euell 61), Downing (Cattermole 84), Yakubu (Craddock 84), Sanli
The next game is tomorrow away to Carlisle and then on 4th August Boro are at home to AZ Alkmaar. Tickets for the latter game are £10.