Polesitter Leclerc was passed by Max Verstappen and eventual Baku victor Sergio Perez come only lap six of 51, with the Ferrari driver opting not to fight the Red Bulls to preserve his Pirelli tyres.
The Monegasque eventually finished 21 seconds adrift of Perez but held off Aston Martin driver Alonso by 0.8s to end the two-time champion’s run of consecutive podiums at the start of the year.
Alonso reckoned Leclerc was “lucky” to hang on as late overcast conditions meant temperatures cooled to help Leclerc manage his hard tyres, with Ferrari having already shown tyre preservation struggles so far this season.
The Spaniard told Sky: “I think they got lucky. The hard tyre was less degradation than expected.
“We put the hard tyre on when the safety car came [for AlphaTauri driver Nyck de Vries clipping the Turn 5 inside wall]. It was 38 laps to the end.
“It held on quite OK and also [there] was some clouds at the end so track temperature was dropping.
“I think with the mediums, the Ferraris had massive degradation in the first stint.
“On a normal hot race, I think they will struggle a little bit more. Today was good for them but Miami [next race, humid conditions] is going to be different.”
Alonso also took aim at his former employer for its Azerbaijan performance, saying that a difficult weekend for Aston Martin - owed to intermittent DRS failure and compromised car set-up - was only marginally slower than Ferrari perfection.
He continued: “The summary of the weekend is that Aston had a tricky Baku weekend with the DRS problems and the set-up.
“We were not that fast in any of the sessions and we’re still 1s from the podium.
“Ferrari, they had a perfect weekend: pole position for the main race, pole position in the sprint race, super-fast car. They were just 1s from the Astons so overall we have to be happy.”
Alonso drew attention in the race for flagging the benefits of a tweaked brake bias setting, instructing his race engineer to pass on the advice to team-mate Lance Stroll.
This gesture, Alonso said, reflected everything “working perfectly” within Aston Martin.
He explained: “The job that everyone has done in Aston Martin is extraordinary.
“Between Lance and me, we are aware of that. We are trying to help the team as much as we can.
“If we find something on the car that we didn’t spot in the strategy meeting, we try to share it immediately by radio.
“At the moment, everything is working perfectly, and this is our strength probably - and that’s why we are second in the constructors’ championship: because we think only of the team.”