Ricciardo was initially 12th in Q1 and thus safely through to Q2 before losing his lap time to a track limits offence, which dropped him down to 18th.
However, even without the penalty he couldn't match the pace of Tsunoda, who progressed through the three sessions to qualify eighth.
The Australian, outqualified by his team-mate in every event so far this year, admitted he was left "puzzled" at his failure to match Tsunoda.
"The lap itself I was happy with," Ricciardo said. "From my side, I felt like I got everything out of it. And then when I saw it still wasn't good enough, let's say, compared to Yuki.
"I'm still a bit puzzled because I know what those laps normally mean. So, I crossed the line, being like 'Yeah, that was a good one'.
"Obviously, the time got deleted, but the lap itself was definitely the best quali lap I've done this year.
"And going into Q2, I don't know where there was much more time. You obviously take a couple of tenths from track evo. But six, seven tenths? That's not in it."
He added: "I knew at the time Turn 4 I was fighting it. And I remember taking more kerb than I usually am.
"So I knew I was wider than normal. But it's funny, you do it and then already after Turn 5 I forgot about it.
"So I did the lap. And then eventually when Pierre [Hamelin, race engineer] told me honestly, I forgot all about it. So I think it took a while for it to sink in."
Ricciardo insisted that he felt happy with the car in Melbourne.
"I feel confident in terms of braking and balance and all that," he said. "So it's not like, say, [at] McLaren, where I was a bit unsure and all 'I can't really push the car here'. Some corner speeds I see, I'm simply just not able to carry that speed."
He added: "I feel like I'm at the edge with the car in terms of like, pretty much four-wheel sliding. So it's balanced. And I feel now I'm at the limit of where its potential is."
Ricciardo also revealed that the team changed some parts on his car following the last race in Jeddah in an attempt to address concerns he expressed there.
"After Saudi, we saw some things across cars," he said. "The team changed quite a lot and gave me quite a few new parts for this weekend to address some of those issues and concerns.
"And it looked like it was better. But I still, let's say, I'm still not fully convinced, because like I said, we still feel like we're struggling more than we normally are in a car that I'm pretty happy with."
