The 63-cap Australia veteran came through the match unscathed but conceded he found it hard to make an impact.
"I really did struggle," said Mortlock. "I always knew that match fitness would be a little bit down but I found it tough to get involved.
"Obviously it's the first time I've played with a lot of these backs so the cohesion was lacking.
"We've got a lot of work to do over the next week or so."
Mortlock acknowledged the Brumbies' performance was not up to scratch but paid credit to the Chiefs.
"We caught a Chiefs outfit that really were on their game," he said.
"We knew going into this game we couldn't afford to give them turnover possession and that's exactly what we did and we really paid for it."
The one positive was his reconstructed shoulder stood up to the challenge of Super 14 action.
"The shoulder's fine," he added. "Leading into this match I was always really confident the shoulder would hold up okay, it was totally fine."
Brumbies coach Laurie Fisher was full of praise for his returning captain, however, but was less satisfied with his team's overall performance.
"He (Mortlock) did some wonderful things and he's only going to get better," Fisher said.
"He continues to be our go-to, he made some great yardage and some great touches. It's good to have him back.
"We struggled with the Hurricanes a few weeks ago and we struggled in the same area.
"We've really got to man up and muscle up in the contact area of the game.
"In the end we just got manhandled on quite a number of our carries and that was the difference - their speed and capacity to move the ball."