They were never as convincing in the match at Borehamwood as they had been in the first leg, but their fine performance in Prague ensured that did not cause them any difficulty.
"We weren't at our best, but Prague are a decent side and they weren't going to make it easy," said manager Tony Gervaise.
"We knew it would be untidy and scrappy. We huffed and puffed in the first half, but we improved in the second half and our quality came through."
The result put the Gunners within two games of reaching the new competition's first final, to be played in Madrid next May.
The Champions League has replaced the Uefa Cup, which Arsenal won in 2007 and in which they reached at least the quarter-finals in the seven seasons they took part.
"The team's consistency in the Uefa Cup was fantastic," said Gervaise. "And now we want to go as far as we possibly can in the Champions League.
"Whoever we get in the quarter-finals will be tough because they'll be one of the best teams in Europe. But so are we - and we fear no-one."
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