The Premier League club went ahead after only three minutes when midfielder Johnson headed home a Robert Snodgrass free-kick.
And shortly after the re-start the 26-year-old was at it again - this time powering home a header from Javier Garrido's pinpoint cross.
However, despite the win, there was real concern for City boss Chris Hughton after the game, with new signing Hooper carried off on a stretcher early in the second half with a shin injury.
The close-season arrival from Celtic went down after rolling defender Gordon Schildenfeld in a challenge and was subsequently taken to hospital for precautionary X-Rays.
That incident aside, the visiting Greek team played their part in an open contest, with Anastasios Lagos narrowly shooting wide of John Ruddy’s far post on the quarter-hour mark as they searched for an equaliser.
They went even closer when Schildenfeld's effort was blocked on the line and then a follow up header rebounded on to the crossbar.
Prior to his departure, Hooper had looked lively, and he went close to scoring when he was picked out in the box, but the striker slipped over at the crucial moment and the visitors cleared.
Norwich wrapped up the win after 58 minutes when Johnson headed home his second, while substitute Nathan Redmond could have added gloss to the scoreline late on with a stinging low drive that goalkeeper Stefanos Kapino parried wide.