"He always tries to stay on the shoulder, looks in behind and he's a quick player. By making those runs in behind defenders it creates a bit more space for you in front of them.
"So it's working well at the minute."
When asked if Hernandez was the buy of the season, Rooney replied: "I think so, definitely. He's been fantastic and works so hard as well. He wants to improve and it's good to see."
Rooney, who was playing in a deeper role behind the Mexican forward, also impressed with some superb passing and Ferguson was quick to hail the partnership.
"It has been developing well," stated the 69-year-old Scot. "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."
My feeling is one of regret, we let our chance slip. Manchester United are not a fantastic side and were not at their best but we could not capitalise on that
Marseille coach Didier Deschamps
The downside for United - still in contention to win the Premier League, FA Cup and Champions League - was the loss of defenders John O'Shea and Rafael to injury.
United were already without captain Nemanja Vidic because of a calf problem, which meant centre-backs Chris Smalling and Brown played only their 10th game together, with O'Shea starting at right-back and Patrice Evra on the left.
O'Shea was taken off on 36 minutes when he pulled up clutching his left hamstring, while substitute Rafael was also taken off with a thigh problem and replaced by his brother Fabio on 69 minutes.
"It was nervy because so many players came off with injuries," added Ferguson. "It shifted the balance of the team.
"I would have rather brought on Darron Gibson because the problem was always going to be [Marseille's] height and it caused us problems.
"In defence it was maybe a lack of understanding between the players.
"We have changed the back four many times and without the experience of Nemanja Vidic or Rio Ferdinand you are going to be under pressure at times with the young players we have."
Marseille coach Didier Deschamps was disconsolate after the defeat, particularly as his team had two good chances to score, first through Andre-Pierre Gignac and then Souleymane Diawara.
Deschamps said: "My first feeling is one of regret. We let our chance slip and we are out.
"Manchester United are not a fantastic side and they suffered two injuries during the game. They were not at their best but we could not capitalise on that.
"But we are a young side, who are learning, and it will take time. At this level small details win you games.
"Our aim at the beginning of the season was to get to the last 16 and we have achieved that. So in a way we have done reasonably well."
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