Ferrari were by far the quickest throughout practice but when the rain fell Mercedes took full advantage to claim a one-two lockout at the front of the grid.
Hamilton will start from pole position while Mercedes team-mate Valtteri Bottas secured second place.
Kimi Raikkonen and Vettel make it an all Ferrari second row but the German trails Hamilton by 17 points in the Drivers’ Championship so he will be desperate to overtake his rival at some point in the race.
But starting behind the Brit is not the worse outcome for Vettel.
“I don’t think today was awful and it’s not a disaster to start third and fourth – the gaps weren’t huge to Mercedes – but certainly we would have wanted to be ahead in the dry,” he said.
“In the dry it could have been a different outcome but it wasn’t dry, so we need to make sure we are always up there [in all conditions], so there is still work for us to do.
“Obviously when it’s wet everything feels a bit different and then we are not as competitive in the wet as we are in the dry.
“But in these conditions anything can happen and obviously you see the gap is quite big at times and in the end it came down to the final lap and I pushed quite hard and tried everything.
“Maybe it wasn’t the tidiest lap but it also wasn’t awful, so I’m pretty OK with the result.
“Obviously I would like to be further up, but that’s what we have now and for tomorrow we start with a clean sheet of paper and room open for strategy for everyone.”
Vettel will be hoping the rain stays away on Sunday to allow his Ferrari to perform to the best of its ability.
Even in the wet conditions, he was only eight tenths of a second behind Hamilton so if it remains dry he has a strong chance of coming out on top.