Alonso switched from his old hard tyres to mediums as the first signs of a shower hit some areas of the track.
After it intensified and spread over the whole circuit, he quickly came in again for intermediates.
Alonso held onto his second place, but Krack insists that had the Spaniard made a single stop instead of two he still wouldn’t have beaten race winner Max Verstappen.
He stressed that the Silverstone outfit made the right call with the available information at the time.
"We need to look at the whole thing, how it went,” said Krack. “Obviously, you try to stay out as long as you can in such conditions when you do not really know what's going to happen.
“We did not anticipate so much rain, to be honest. So we thought that it would just be a short shower, and drying quickly because the track was very hot. Then normally, you would say, okay, we stay out one more, two or three more laps, but the tyres were worn already quite a lot.
“And we saw the temperatures going down. So that was a bit of a risk. When the car came in then with this information, we said, okay, let's fit the mediums. But then when the car left, shortly after we saw that it was really a lot of rain. And we had to come back."
Krack admitted that the team hadn’t expected the rain to intensify in the manner that it did, and didn't think it was wet enough for the inters to last.
"Honestly, we thought we could go to the end with the mediums because it will dry quickly,” he said. “But then we misjudged a bit that it was raining because in this part of the track [the pitlane] it took very long before it started to rain.
“And also this area, it rained the least. So probably that was a bit a misjudgement, because we thought also that the inters would wear down massively in this part of the track.
“At the end of the day, it was a conscious decision to go on the mediums. And we saw then a lap later that it was not going to work. And we decided to call him back."
Krack said Alonso didn’t lose victory with the call: "No, I don't think it was lost. Because if we had fitted intermediates Max would have fitted intermediates as well. And also he had the gap. So I don't think it would have changed much.
“I think overall we must not be too greedy, we should look back and see what were our objectives. We came here to do better than what we have done so far. I think this we managed. And I think the Red Bulls were a little bit too fast for us."
Krack also noted that it was safer to stick with the call for slicks rather than make a last-minute change, which might have led to a mix up.
“As I said, these calls are made in a very short amount of time. And then you have to live with it, when you have decided, you have to execute. Because otherwise you have two wets and two slicks on the car.
“So once you have made the call, you have to execute. Because anything that you try to revert, then it will go completely wrong. We will look into it, we will learn from it, and we try to do better next time.
“We have quite a good understanding between driver and team. And sometimes the driver says you go with it. In this case we decided to fit the slicks. Fernando was happy with it. And then after he was also happy to have the inters back on!”