The video referees took an age to confirm the touchdown, which sealed the Warriors' fifth win of the season.
It was a courageous effort by the visitors, who lost Ryan Hoffman (concussion) and Thomas Leuluai (knee) inside the first 20 minutes which forced the other forwards to play many more minutes than they would have anticipated.
The Warriors seemed to tire badly in the second half, as the Eels came back into the match in a big way.
Parramatta scored three unanswered tries in the second half, and only poor goal kicking from Luke Kelly (0/3) prevented them from taking the lead.
The Warriors led 12-0 at halftime but it probably should have been more. The Eels, who had won just one of their last five matches, were down on confidence and it showed.
They were plagued by bad decisions and poor execution and completed at just 47 per cent in the first half. Parramatta were trapped in goal, forced over the sideline, passed to the 'invisible man' with the try line beckoning and even came up with a top class 'falcon'.
It wouldn't have made for easy viewing for coach Brad Arthur, nor a certain Kieran Foran, who must be wondering what he is walking into next season, when coupled with the ongoing dramas at board level.
The Auckland club were good enough to capitalise. They weren't short of errors themselves, with Chad Townsend, Solomone Kata and Ken Maumalo all guilty of loose carries at crucial occasions in the first half. But they got away with it and Shaun Johnson was the inspiration for some early magic. He produced a lovely cut out ball to set Jonathan Wright free, then an improbable pick up at full pace from the winger's clever kick.
But what about what happened next? Just like last week, Johnson stepped through a maze of defenders, like a grasshopper leaping between daisies. It's hard to think of a better side stepper in the history of the game - not Brett Papworth, not Allan Langer, not Henry Paul.
There was physical intent from the Warriors - the 105kg Semi Radradra being forced back into his in goal epitomised that - and clean execution, as Townsend came up with a wonderful cut out pass to allow Kata to power over for his eighth try of the season.
Unfortunately for the visitors, everything turned in the second half. With just 15 available players, they were always going to tire but they didn't help themselves. Wright dropped a bomb on his try line to allow Anthony Watmough to dive over and begin Parramatta's comeback.
Moments later newly installed centre Dominique Peyroux misread badly to allow Semi Radradra to score near the right sideline. When Ryan Morgan scored the Eels third try in the 63rd minute the Warriors looked unlikely victors but pure grit on defence followed by Thompson's heroics saw them home.
Warriors 17 (S.Johnson, S. Kata, B. Thompson tries; Johnson 2 goals, C. Townsend field goal)
Eels 12 (A Watmough, S. Radradra, R. Morgan tries; L. Kelly field goal)
Halftime: 12-0
