Defender Bonucci often found himself in the role of replacement playmaker for much of the evening as the French side worked hard to shackle Andrea Pirlo’s influence from deep.
His persistence was rewarded in the 85th minute as he lashed home after Paul Pogba bundled a poorly defended corner goalwards.
Juventus substitute Mirko Vucinic - on for injured top scorer Carlos Tevez - cut a particularly relieved figure having blazed over from close range a minute earlier.
Jimmy Briand wasted Lyon's best chance and botched a clear opportunity on the break alongside Steed Malbranque shortly before Bonucci's strike to ensure boss Remi Garde suffered an unsatisfactory 48th birthday.
Juventus' midfielder Kwadwo Asamoah shoots the ball. Photo by JEFF PACHOUD/AFP/Getty Images
Basel took a huge step towards the last four with a 3-0 win over Valencia.
In a game played behind closed doors at St Jakob-Park after Basel fans' misbehaviour in the victory at Red Bull Salzburg in the last 16, the hosts made light of the lack of home support to give themselves a great chance of a spot in the semi-finals for the second year in succession.
A first-half brace from Matias Delgado - a rasping effort in the 34th minute and a beautifully guided close-range finish four minutes later - and Valentin Stocker's impudent stoppage-time chip put Murat Yakin's side in complete control of the tie heading into the second leg in Spain next week.
Valencia's forward Eduardo Vargas vies for the ball with FC Basel's forward Breel Embolo. Photo by FABRICE COFFRINI/AFP/Getty Images
Porto lived up to their billing as favourites against Sevilla with a deserved 1-0 win.
Coach Luis Castro said in the build-up that Porto's status as favourites in almost every game they play has hampered them this season - the reigning Primeira Liga champions sit third in their domestic division, 15 points adrift of leaders Benfica - but they put in a commanding display at Estadio do Dragao on Thursday.
After dominating the early stages, Porto finally took the lead just after the half-hour mark as captain Eliaquim Mangala powered a diving header in from an audacious Ricardo Quaresma cross.
A below-par Benfica showed their European nous against AZ to clinch a 1-0 victory and seize the advantage in their tie.
Jorge Jesus' men have reached the semi-final and the final of the competition in their last two attempts and look on course to go one better this term after a hard-fought away win in the Netherlands on Thursday.
Sevilla's midfielder Vicente Iborra de la Fuente vies with Porto's forward Jackson Martinez. Photo by MIGUEL RIOPA/AFP/Getty Images