The 27-year-old Croatian forward headed to Ukraine in a £6million deal during the summer after finding himself down the Gunners order following the free transfer signing of Marouane Chamakh.
Eduardo had vowed not to celebrate should he get on the scoresheet against his old club - and was true to his word when netting a fine volley with seven minutes left after coming off the bench.
The Gunners fans, however, created a unique moment of sportsmanship in applauding the goal, which clearly touched the striker, whom Arsenal had signed from Dynamo Zagreb in July 2007 for a reported £7.5million.
"It was unbelievable", Eduardo told Arsenal TV Online.
"It was like I still play for Arsenal, when I came back and they started to call my name. It was fantastic."