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 their opponents and Terry was keen to underline the below-par nature of the performance.
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"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 they prepare 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."
Despite the likelihood of fixture congestion as the season goes on, Terry says that his team-mates are keen to win the Europa League following the disappointment of being the first holders to be knocked out of the Champions League at the group stage.
He added: "We were very disappointed to be out the Champions League and to be watching it Wednesday and Tuesday nights.
"It’s disappointing but that's enough motivation for us to kick on in this competition. We're in it to win it and nothing changes from that."