Fernando and Stoffel will start in 15th and 18th positions respectively for the season finale of 2018, and the final Formula 1 race for both drivers with McLaren.
With FP3 taking place in different track conditions to qualifying, both drivers worked hard to set up their cars for the cooler temperatures to come, and Fernando finished in 15th and Stoffel in 19th.
Qualifying was all about reacting quickly to rapid track evolution as the sun began to set. Both drivers had clean runs and their times progressed with each lap they did. Despite the improvement on his final lap, Stoffel missed out on progression to Q2, qualifying in 18th. Fernando had a solid final run and managed to squeeze through into Q2. There, he wrung out all the performance he could, and will start tomorrow's race in 15th.
Fernando Alonso: "We weren't optimistic at all about our chances of making it into Q2, as we haven't been too competitive in any of the sessions so far this weekend, so it was a nice surprise. I was pushing quite hard on that qualifying lap - it felt good.
"We start five positions away from the points tomorrow and hopefully we can benefit from some action in front of us. On pure pace we're maybe not in the top 10, but who knows tomorrow.
"Outside the car there's a lot of things happening this weekend: a lot of emotions and a lot of nice touches here and there. Tomorrow when I put the helmet on and jump in the car I'll treat it like the last one, and I'll try to enjoy it and do my best."
Stoffel Vandoorne: "Today was a bit better than yesterday. It was my final qualifying of the year and it was all about having fun and enjoying it as much as I could. I know we've not been in shape all season really, so we did the best we could. Tomorrow, we're going to try and make the most of it, have a good start and a good opening lap, and then see what happens.
"It's never easy to go from FP3 into qualifying where the track temperature is so different. I think it's actually a nice feeling to go that way as you gain a lot of performance, but it's the same for everyone.
"I had a lot of fun out there today and tomorrow I'm going to enjoy it as much as I can too. I've had a good couple of races lately and I hope that continues and I can finish the season on a high - that's what matters.
"These cars are still nice to drive, even though sometimes when you look at the classification it's not always what you want to see. On the other hand, I'm looking forward to seeing the chequered flag tomorrow and starting a new chapter. I have mixed emotions about tomorrow. It's sad to leave so many people I've been working very closely with, but I'm also quite excited for the future."
Gil de Ferran, Sporting Director: "Given our qualifying pace this year, coupled with the ever-changing track conditions from session to session here in Abu Dhabi, it was always going to be particularly difficult to predict where we would end up today.
"Stoffel had a clean run in Q1, and although he made progress on each of his three flying laps, it wasn't quite enough to make it into Q2.
"Thanks to a bit of magic from Fernando, who was able to put a flawless lap together on his final run, we progressed through to Q2.
"Unquestionably, whatever happens tomorrow, it will be an emotional day for all of us, as it marks the end of a challenging year for the team. We say farewell and thank you to Fernando and Stoffel, as well as commemorate the end of a chapter in the legendary career of our double world champion.
"We'll fight on together for the last time and will see what tomorrow brings at this spectacular venue."
Check out our Saturday gallery from Yas Marina, here.