The visitors arrived at the Rams' home ground needing a win to guarantee a return to the top flight, and when Fabio Carvalho put them ahead in the 20th minute it looked as if the script was being followed.
But teenager Luke Plange – loaned back to Derby after being signed by FA Cup semi-finalist Crystal Palace in the January window – levelled matters after the break before an own goal from Tosin Adarabioyo in the 73rd minute put the home side into a lead that it would manage to hold on to.
Plange was at the heart of that goal too, pressuring Adarabioyo as the ball was whipped into the six-yard box, and he could prove to be a key figure for the Rams as it desperately tries to maintain its Championship status.
Occupying the first of the relegation spots after its 21-point deduction by the EFL for historical financial irregularities, Derby remains above Peterborough and Barnsley, which also won on a busy day for the league, but Reading is still nine points above the Rams in the safety zone and also won a dramatic encounter away at Sheffield United 2-1, the winner coming in the second minute of stoppage-time after the Blades had equalised in the 90th minute.
"We knew it would be a tough game, but I believed we would win," Rooney said after the match.
"When I saw Reading score in the last minute, you are worried young players were watching that and it would take energy out of them. But I felt at half-time if we had more belief, we would win. The character of the players is incredible.
"The mentality is the thing I am most proud of. But we have to change the away form if we are to have a chance of staying up."
Derby has just four matches left in the season, two of which will be away at Queens Park Rangers and Blackpool. Its other opponents are Bristol City and Cardiff City, both of which will travel to Pride Park.
For Fulham, it will have to wait to celebrate what will surely be another promotion to the Premier League. The Cottagers have been the runaway leaders for much of the campaign, and are nine points clear of second placed Bournemouth, which could only manage a 0-0 stalemate against Middlesbrough on Saturday (AEST). Fulham has scored almost 30 more goals than the Cherries through the campaign to date, and need just five more to crack 100 for the season.
"Our first-half was good and in the second-half, we expected a reaction and it was important for us to control the game and we made a mistake," Fulham boss Marco Silva said.
"We had chances to win. We are at the top of this league for a reason but we lost our focus. We have to improve. We knew before the match it would be emotional. We knew what would happen with three points. Derby’s pressure is much tougher. Our pressure is the nicest pressure. But if we want to play in the Premier League, we have to deal with pressure."