Hooper went down clutching his ankle early in the second half, but it failed to prevent his side from picking up an impressive win over the Greek outfit.
The Canaries got off to the perfect start when Johnson was on hand to head home from a free kick from Robert Snodgrass.
Johnson nearly netted again soon after, before Hooper fired the ball just wide of the post.
Gordon Schildenfeld almost offered a reply for Panathinaikos but his shot was blocked on the line.
Norwich doubled their lead just before the hour mark when Johnson headed his second goal of the game, this time from a Javier Garrido cross.