This was a stuttering performance by the Red Devils, with their best football coming in the last 20 minutes when Rooney and Paul Scholes replaced Carlos Tevez and Anderson.
Bolton, whose last win at Old Trafford was six years ago, seemed to set their stall for a point and a draw looked possible until the United penalty on the hour.
Tevez found Ronaldo on the right side of the Bolton box but, as the Portuguese winger moved across the penalty area, he went down under a good tackle by Jlloyd Samuel.
The game looked set to continue until referee Rob Styles pointed to the penalty spot - a decision which seemed to take all the players by surprise.
Ronaldo, starting his first league game of the season, stepped up to send goalkeeper Jussi Jaaskelainen the wrong way with his right-footed shot going into the net to the goalkeeper's left.
If United's first goal was ridiculous their second was sublime.
Rooney raced down the left from just inside the Bolton half. He fed the ball to Ronaldo in the penalty area and he back-heeled the ball to Rooney.
The England star took the ball in his stride 12 yards out, side-stepped Bolton skipper Kevin Nolan and curled a glorious left-foot shot into the far corner of the net beyond Jaaskelainen's despairing dive.
United created the best chances, but found Jaaskelainen in superb form.
The Bolton goalkeeper produced the first of a string of fine saves in the 15th minute when he hurled himself across goal to touch away Tevez's crisp shot from the edge of the box, with Ji-Sung Park hitting the rebound into the side-netting.
Ten minutes later, Jaaskelainin was again springing across his line this time to keep out Ronaldo's stringing 25-yard free-kick.
Jaaskelainen did well to tip over Anderson's 34th minute cross-cum-shot from the right, but Bolton should have taken the lead four minutes before the interval.
Gretar Steinsson's cross from the right caused problems in the United penalty area when Kevin Davies challenged Rio Ferdinand.
The ball rebounded to Fabrice Muamba, who shot wide from eight yards with the goal at his mercy.
Ronaldo was denied by a post four minutes after the restart when his shot from 12 yards hit the woodwork after Bolton defender Andy O'Brien failed to clear Gary Neville's cross from the right.
Then came that penalty and Rooney's sublime second to secure the points that might just kick-start United's title defence into life.