After the race was resumed following the red flag, drivers soon began to move from wet to intermediate tyres, with most coming in at the end of the second flying lap.
With his teammate Ocon coming in on that lap, Alonso was told to stay out so that Alpine wouldn't have to double-stack him.
When the Spaniard came in on the next lap, Daniel Ricciardo was the only other driver who was yet to stop, and Alonso ended up losing ground and two places.
Later and with all drivers struggling to keep their intermediate tyres, Alonso wanted to pit for a fresh set in the closing stages of the race, believing that he would have the pace to make up for the stop and still pass cars up ahead.
Zhou Guanyu and Lance Stroll, both of whom had little to lose at the rear of the field, were the first drivers to go for new tyres, on laps 18 and 20 respectively.
Alonso was running in seventh place when he was finally allowed to come in on lap 22. He lost several positions, but he had the speed with which to recover his seventh place.
At the end of lap 28 he just failed to pass Sebastian Vettel on the run out of the final corner – and was met with the chequered flag, which came out earlier than teams expected as the three-hour limit was passed.
It was anticipated that there would be one more full lap after the first time the leader passed the flag after the three-hour mark.
"The strategy didn't work for us today," said Alonso. "We made the wrong choices continuously. First, we stopped the last to put the intermediates, we lost places.
"Then we stopped too late for the second stop with six laps to the end, and I just finished in the same place what I was. I was asking to pit earlier on both occasions, but today my microphone maybe didn't work."
Asked by Autosport if he had to trust the team, he said: "We should have stopped 10, or 11 or 12 laps to go. As I said, I don't know what they were doing, and then we stopped six laps till the end. We lost an opportunity."
Alpine sporting director Alan Permane said the team was caught out by the flag coming out a lap earlier than teams had been anticipating, and that Alonso would have passed Vettel and thus gained one place as a result of the tyre change.
"I think the race was stopped a lap earlier, the chequered flag was a lap earlier than it should have been," said Permane. "I think when Max crossed the line, there were about five seconds still on the clock, and then they chequered flagged it the next lap."
Regarding the timing of Alonso's stop, he said: "Had the race gone to the distance we thought it was going to go, would he have got Sebastian? Yeah.
"So probably we should have done it a little bit earlier, although it's not easy to say, because his tyres were going away as well on that stint.
"And so in hindsight, yes, we could have. But I don't think we realised quite how easy it was going to be to overtake people.
"He was talking about it earlier, should we think about pitting? And he would have had to take five cars, and we thought that's not going to be good.
"And then I think we saw Zhou pit, and he was five seconds a lap quicker. And we said, 'Okay, yes, let's do that.' We will need to look at it. But for sure if the race had gone on lap longer, which I think it should have done, he would have been in front of Sebastian."
