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.
Source: Autosport