Whilst a Red Bull top two looked likely, Charles Leclerc completed a blistering lap at the last minute to steal P2, and therefore the top spot on the grid for the race.
Sergio Perez re-discovered his form at just the right time this weekend, and qualified P3, meaning he will start the grand prix on the front row.
Finally, it was Alpine who offered the biggest surprise of the session, with Esteban Ocon reaching Q3 ahead of starting P9 after Verstappen's penalty.
Here's what the top three had to say in Belgium...
"It was a nice qualifying. Luckily the weather was okay. It was just raining a little bit and at least we could do a decent qualifying.
"Everything worked well. Every tyre set that we were on we could just do good lap times. I was thinking about Q3, not knowing if it was going to dry out, so I was trying to keep two new sets for Q3, and luckily we escaped Q1 and Q2.
"Very happy. The car was working quite well in the wet. I could just do my laps and try to do clean lap times in the wet, which is always quite tricky.
"But tomorrow, of course I know that it’s quite a different day. It’s going to be warmer, normally no rain, so it’s all about tyre degradation. We just need to make sure we’re good on that.
"I know that I have to start 10 places back so this was the best I could do today, and I go from there. I don’t know how quick we’re going to be. I hope that we can be in the mix to try to move forward.
"The race can be lost in Turn 1, so just need to see what happens at the start, naturally, and just go from there. It’s a very long race, it’s very hard on tyres and we just need to try to manage that as good as we can, and hopefully then we can be competitive tomorrow.
"We are not making it easy on ourselves and especially of course in the battle that we’re in. I know that today was a great day, but it’s in the wet, we need to be quick in the dry tomorrow. It’s going to be a tough battle. We’ll try to do the best we can. Hopefully we can battle the Ferrari and Mercedes ahead, and if we have a bit of luck, maybe we can challenge the McLaren."
"It's good. I definitely did not expect that this weekend. Obviously with the tricky conditions we could do something above our expectations.
"So it's a good day for the team so now we need to focus on tomorrow and see what will happen when the rain is gone.
"Without this rain, probably P5 was the position we were fighting for with the Mercedes especially. But with the rain it helped us a little bit, but I'm not going to complain.
"I'm really happy, I'm really happy with the lap in Q3, and it's good to be back on the front part of the grid. Now we've got to finalise that tomorrow.
"It's not the easiest first place to keep on the first lap here, but honestly I will see. Every start is different and then once I will be in the car tomorrow through Eau Rouge I will see what the best thing is that I can do.
"It was very tricky, at times. As always in these conditions, it’s so easy for it to go wrong, as it’s been going in the last few qualifyings in these conditions. It was good to finally put it together.
"Unfortunately we didn’t have any new tyres for Q3. We were a bit out of sync in Q2, so we were also quite lucky to make it P10.
"I think P2 is probably the best position you can wish for in Spa. It was the same with Charles last year, so I’m going to be trying tomorrow to be the same. It’s a long race ahead of us. It looks like it’s going to be dry, so we’ll see.
"Like I’ve always said, every weekend is a new opportunity to do better, every day. Tomorrow is a new opportunity for us to do even better than today and go for that win.
"We’ll see. It’s a very long race ahead of us. I think degradation will be quite tricky. Graining with this new tarmac. I think there a lot of unknowns still. But I’ve got a good feeling for tomorrow, so we’ll see."