Both Van Persie and Kagawa were on target at Old Trafford as United came from a goal down to win 3-2 and register their first Premier League victory of the season.
"I was pleased with both of them," Ferguson told MUTV. "It's early doors and they'll have a better understanding as time goes on."
However, Ferguson was not happy with United's lack of urgency in the second half and admitted that they "struggled" after Fulham scored their second goal to reduce the deficit to 3-2.
"After cruise control, we made a terrible mistake for the second goal and it became a match," he said. "It should never have been a match, some of our football was fantastic. But we lost that second goal when we should have been in easy street.
"Fulham tried to slow the tempo of the match down. They do it very well because they've got several players over 30 years of age. They're a very experienced team.
"After their second goal, we struggled."
United's next Premier League game is against Southampton away from home next Sunday.