Hernandez showed a poacher's instinct as he grabbed two goals from close range but Marseille made it a nervy night at Old Trafford thanks to Wes Brown's own goal eight minutes from time.
After sealing progress to the last eight for another year, Ferguson said how pleased he was at the blossoming understanding between his two young strikers.
"It's been developing well,'' he said. ''Where Wayne has been playing in the past couple of games he is a real threat. He has such power and speed and Hernandez is unbelievable with his movement. The boy has goals in him.''
United's win came at a cost though, with defenders John O'Shea and Rafael both forced off with what appeared to be hamstring injuries. That forced Ferguson to make substitutions he felt unsettled his team and contributed to an anxious end to the game.
''It was nervy because so many players came off with injuries,'' he said. ''It shifted the balance of team. I would have rather brought on Darron Gibson because the problem tonight was always going to be height and it caused us problems.''
Ferguson said he hoped Nemanja Vidic would be fit for the weekend, after missing the game through injury. ''We'll have to wait and see,'' he said. ''Jonny Evans started training this week so hopefully he will be back.''
Rooney admitted he was relieved to overcome a stern test of United's Champions League credentials: He said: ''We are delighted to be through to the quarter-finals. It was a difficult game, we knew they were a physical team with a lot of power - we just deserved it in the end.''
Rooney laid off the pass that allowed Hernandez to open the scoring after five minutes and put United ahead in the tie after the first leg finished goalless. The England striker admitted he enjoyed playing a slightly withdrawn role behind his young team-mate, who has now scored 16 goals in his debut season, and was preferred to Dimitar Berbatov.
''He's got great movement so I'm playing the position that I did when I started playing professionally. I'm enjoying it and thankfully he's a finisher,'' Rooney said. ''It's not often forwards get the chance to be on ball and enjoy playing. I enjoyed tonight.''
He added: ''Our gameplan was to attack them first half and to get a goal or two up. We managed to get one and we held on. 'We were unfortunate to concede the goal.''
Rooney said he would be happy to meet Barcelona in the next round, adding: ''If you want to win the tournament you need to play and beat anyone. 'Whoever we get next we'll be confident we can beat them.''
Asked if the result would have been different if they took those chances, OM boss Didier Deschamps said: ''I am sure. 'My team have young players but after they have done well, and we had good opportunities, we don't score. Then when it was 0-2 it was more complicated for us.''
He added: ''The players felt it was possible (to win) because Manchester was not fit physically. A lot of their players missed this game through injury, it was not the best team of Manchester. We tried but it was not enough for us today.''