After Rooney's achievement, Ferguson believes that the striker is on his way to surpass Sir Bobby Charlton's legacy at Old Trafford, by breaking the club legend's tally of 249 goals for the Red Devils.
"That's a tremendous level to talk about [matching Charlton]," he told ESPN. "I think that's a fantastic achievement considering he's only 25 and he's got many years in front of him, so I'm sure he'll pass it."
The manager was also impressed with the combination of Javier Hernandez and Rooney upfront, gushing: "It was excellent. They're a constant threat, the movement and the pace they play at was truly first class for us."
"We kept playing our football, that's what we're here to do," he added. "We're better at that and withstood all the challenges and just got on with it."
The Scot also gave praise to Phil Jones for his quality since moving from Blackburn in the summer transfer window.
He continued: "He's an exceptionally good young player and he's improving all the time, and he can play anywhere really.
"He can play midfield, he can play right-back, centre-back as we know, but I felt that Chris Smalling having an arduous time with England games...I just thought [we'd] freshen it up a bit and bring Rio's experience back into the team and I thought they did very well."
While Manchester City also beat Wigan 3-0, Ferguson was loathe to bother with their results.
"I think you just have to concentrate on yourselves," he concluded. "We've got a lot of difficult games and it's a difficult start to the season we've got, we've got all the bigger names and we've got Chelsea next Sunday, so it's a hectic time and if we can come through it we'll have done well."
"I'm obviously delighted to score a hat-trick, and first start with Chicharito [this season] and to both score is great," Rooney added.
"We always know Bolton's a difficult place to go, and we got the early goal and kicked on from there really, [we] controlled the game and could have scored more really."