England went into the international break level on points with Montenegro at the summit of Group G but ended it six clear and knowing a draw in next month's top-of-the-table showdown would seal their place in Poland and Ukraine.
"It's a nice to get the six points and more or less have one foot in the finals," said Rooney.
"It was a tad frustrating at times but the result was the most important thing and we're thankful for that."
Wales went into Tuesday night's game on the back of an impressive win over Montenegro but Rooney admitted Gary Speed's side took England by surprise.
"They did, to be honest - they played really well," said the striker, who watched visiting substitute Robert Earnshaw miss an absolute sitter in the second half, which would have cancelled out Young's opener.
"Thankfully, we held on towards the end to get the win. We weren't at our best."