The Czech side bossed possession at Stamford Bridge and levelled the tie on aggregate after just 17 minutes through David Lafata.
A last-gasp Eden Hazard strike saved Chelsea after a struggle to break down its opponent and Terry was keen to underline the below-par nature of the performance.
"We're disappointed with the way we started that but we're delighted to go through," he told ESPN after the game. "We left it as late as we could and sometimes that’s the best way, but not our best performance but we're in the next round so we're happy with that.
"They had two counterattacks in the last five minutes, which is not what we wanted at all. As I say, we're disappointed. It's not the best but we're through and we're happy with that."
Terry, however, was pleased that his side continued to create chances throughout the game despite manager Rafa Benitez making a number of changes as it prepares to face Manchester City in the Premier League.
"We kept going and going," he said. "In the first 80 minutes nothing went for us, really. We had a lot of attempts on goal and didn’t get them. The persistence from the lads was fantastic, and credit to us.
"It was a great goal from Eden. The manager rested a couple tonight and having the likes of Eden on the bench is great. He's come on and shown great sharpness and got a goal to top it off."