The Spaniard ended Q1 second fastest but as the pace sharpened he dropped to fifth place in both Q2 and Q3, but he still felt the pace jump from Aston's car updates were greater than predicted.
Alonso ran the previous AMR24 car package during Friday practice at Suzuka, with team-mate Lance Stroll using the upgrades to provide comparison running, before both drivers switched to the upgrades - which focused on a revised sidepod and floor area changes.
"Yesterday I had the old package, today the new package. Tonight we will have all the data to confirm that, and to quantify the improvement, but everything felt good in qualifying," Alonso said. "Little bit unexpected, to be that competitive, to be honest.
"Just a couple of hundreds from [Sainz] Ferrari, Leclerc [is] behind us, Piastri behind us and Mercedes. So we were here six months ago - 1.5 seconds from pole position. And now we are four tenths."
However, Alonso isn't confident of maintaining fifth place in the grand prix and will aim to defend from McLaren's Oscar Piastri, Mercedes duo Lewis Hamilton and George Russell plus Ferrari's Charles Leclerc who all start directly behind him.
"Looking back at the first three races, we are very strong in Saturday, [but] not so strong on Sunday, we are maybe out of position to be in top five," he said.
"If I get overtaken by Oscar and the two Mercedes or something like that, I think or I will guess this is normal - and we will fall back to our position.
"Let's see what we can do. I'm very open to whatever the race brings to us. I'm extremely proud and happy of today's job and tomorrow is another day."
Alonso agreed with the sentiment that the F1 pack has closed up in qualifying but Red Bull remains clearly ahead on race pace.
"In qualifying it's true that this year that is everything is so close," he said. "We saw Nico [Hulkenberg], Valtteri [Bottas] today, they are three tenths away or something like that, which is incredible.
"Then in the race, you see the real face of the cars. This is something that we are struggling with a little bit as well, we are very competitive on Saturday, and not so much on Sunday. So our true pace, I think, is Sunday's pace.
"On Saturday, because of the grip of tyres, because of everything, maybe you mask some of the problems."
