It was by no means United's most stylish victory in Europe but their manager Sir Alex Ferguson will not mind one bit after seeing his side equal Juventus' Champions League record of 10 straight home wins.
The pace of Ronaldo and Nani on either wing always looked their most likely route of finding a way through the visitors' well-organised defence and brought them the best early openings.
First Ronaldo broke down the right and left Fabio Grosso sliding in his wake but he failed to pull the ball back in time and was crowded out inside the area.
Darren Fletcher saw a swerving 25-yard shot fly just wide before Anderson linked up well with Nani but failed to make his final ball count.
United were not having things all their own way, however, and Lyon responded with a spell of pressure of their own that saw Kim Kallstrom test Edwin van der Sar with a rasping drive.
It looked like the stalemate would extend until half-time but Ronaldo had other ideas.
Nani fed Wes Brown down the right and although Anderson's shot from his cross was blocked, Ronaldo was first to the loose ball and expertly slotted the ball between the onrushing keeper Coupet and the post. That goal put United firmly in the driving seat but Lyon, to their credit, came back strongly after the interval. Initially, Alain Perrin's side failed to test Van der Sar further with Juninho's shot drifting well wide and Hatem Ben Arfa drilling another effort over.
But the visitors went close to making it 2-2 on aggregate when Keita found the space to smash his low shot against the woodwork with the keeper beaten.
United survived that scare and should have extended their margin of victory before the end.
Rooney latched on to a poor Ben Arfa back-pass but was denied by Coupet's block - then wasted another golden chance when substitute Carlos Tevez put him clear.
Further goals would have put an undeserved gloss on United's night but Ferguson will be satisfied that his side have progressed despite never fully getting into their stride.
Man Utd: Van der Sar, Brown, Ferdinand, Vidic, Evra, Fletcher, Carrick, Anderson (Tevez 70), Ronaldo (Hargreaves 90), Rooney, Nani. Subs Not Used: Kuszczak, Saha, Park, Scholes, O'Shea.
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