Boro struck first in the 66th minute through James Dunne but Rovers fought back and Iain Hume equalised 13 minutes later before joint-caretaker manager Rob Jones rose highest to meet a David Cotterill left-wing corner four minutes into stoppage time.
Smith said: “From our point view, the winner is a really poor goal to concede so late in the game. Through all of our work, endeavour and quality in the game, to come away with nothing again is heartbreaking.
“The front two worked tirelessly and gave us an edge. The midfield won that battle in the middle third and the back four were terrific in the main.
“There’s something not quite right of course, when you concede a goal with 10 minutes to go and end up losing the game.
“It’s something that we have to address. The bottom line is we have nothing to show for what is otherwise a fantastic performance.
“We deserved to be in front, albeit from a wonderful strike and there were one or two decisions made in the game from the referee that were pivotal in Doncaster’s fightback.”
Southampton have announced plans for a two-week tour of China as part of their pre-season preparations for the 2018-19 season.