Although another refereeing decision will grab the headlines following this game, United were superior in every department.
Sir Alex Ferguson rotated his side ahead of the Champions League trip to Aalborg in midweek but it was Bolton - with Johan Elmander operating as a lone striker - who took the game to United.
Ricardo Gardner saw an early shot blocked before Kevin Nolan tried his luck from long distance.
Jaaskelainen was Bolton's busiest player and his first save was a comfortable one when Darren Fletcher picked out Dimitar Berbatov but the £30m striker headed tamely at the Finnish keeper.
Megson rues ref's 'absolute howler'
United - playing their first 3pm kick-off at Old Trafford since New Year's Day - began to find some rhythm and Ji-Sung Park scooped a close-range shot over the top.
Ronaldo then went close with a trademark 25-yard free-kick which Jaaskelainen did well to push wide.
Bolton were pushed further and further back as United took control and the visitors packed all 11 players into their own penalty area for a corner which Nemanja Vidic headed over.
Anderson saw his well-placed curling shot from wide on the right tipped away for a corner after Fletcher's perfect pass.
Fabrice Muamba missed a golden chance for Bolton
But for all of United's possession, it was Bolton who delivered a stark warning moments before the break.
Gretnar Steinsson did well down the right and crossed for Fabrice Muamba who carelessly shot wide from eight yards when he really should have sent Bolton in 1-0 up.
Bolton immediately served up another warning after the restart when Gardener fired a shot inches wide of Van der Saar's right post.
United finally got the breakthrough that they deserved - but it came from an inexplicable decision from referee Styles.
He awarded United a penalty when Ronaldo was fairly tackled by Samuel even though none of the home players or supporters appealed for a spot kick.
Fletcher was full of praise for Scholes
Ronaldo stepped up to slam home a routine penalty but it was hardly surprising that Bolton's dismayed fans were soon singing "1-0 to the referee".
Bolton were devastated and were unable to get back into the game as United brought on Paul Scholes for his 400th Premier League appearance while Rooney replaced Carlos Tevez.
And as the home side surged forward their second goal had an air of inevitability about it.
It duly arrived when Ronaldo charged into the left side of the penalty box before stopping and flicking the ball back to Rooney, who checked inside before unleashing an unstoppable shot into the far corner.
United could have doubled their lead in the closing stages and the only talking point afterwards was that incredible penalty decision.
Man Utd: Van der Sar, Neville, Ferdinand, Vidic, Evra, Ronaldo (Nani 80), Fletcher, Anderson (Scholes 71), Park, Tevez (Rooney 71), Berbatov.
Subs Not Used: Amos, Giggs, O'Shea, Evans.
Goals: Ronaldo 60 pen, Rooney 77.
Bolton: Jaaskelainen, Steinsson, Cahill, Andrew O'Brien, Samuel, Davies, Nolan, McCann, Muamba, Gardner (Smolarek 73), Elmander (Vaz Te 66).
Subs Not Used: Al Habsi, Taylor, Joey O'Brien, Riga, Shittu.
Booked: Elmander, McCann, Davies.
Ref: Rob Styles (Hampshire).
BBC Sport Player Rater man of the match: Manchester United's Cristiano Ronaldo 7.69 (on 90 minutes).
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