Playing without Jozy Altidore and Michael Bradley, who are both away with the United States national team, TFC dropped a 2-1 decision after allowing a late goal by Jordan Allan.
"I think we did well for the majority of the game and I think we had them in a good position," said Toronto forward Robbie Findley. "But we had our chances and it was just the way it ended."
Allen scored in the 89th minute as Real Salt Lake picked up its first win of the season.
The 19-year-old's header from close range came off a feed from Javier Morales from the right wing.
"There was so much adrenaline, and it was just a moment that I've been waiting for so long," said Allen. "It was really just a great moment for me personally and for the team, also, to get the three points."
Allen's goal came just a minute after Toronto (1-2-0) tied the match 1-1 when Jackson took a feed at the top of the box from Bright Dike and used a deft touch to sneak it past an outstretched Jeff Attinella.
Real Salt Lake (1-0-2) opened the scoring in the 38th minute, when Luke Mullholland got behind the defence inside the six-yard box and headed home a long feed from Morales.
"I told the guys we need to control the things we can control, which is ourselves and be better defensively and be confident on how we are going to play," Toronto head coach Greg Vanney said. "The things we can't control have to get better too, but that isn't something we can work on. It is tough to play 7 games on the road."
Both teams had apparent goals waived off. RSL lost one to an offsides call, and Toronto had one disallowed when Nick Hagglund was called for a foul.
"I thought in the second half we dominated the game, for sure controlled the game and found ourselves in good positions," Vanney said. "We scored a goal that was a goal, which is ridiculous. Then we scored a second goal and had a mental lapse."
RSL's Nick Rimando was away with the U.S. national team.
With files from The Canadian Press