Malaysia lost 4-3 in the penalty shootout after a 1-1 draw after 90 minutes.
Maloney said it was another game that his side had dominated without getting the result they wanted.
“We just couldn’t manage to put the ball in the back of the net. So disappointed honestly with the result. My players were undefeated in 90 minutes of football.
“It’s difficult to accept but, again, they played their hearts out and it was a performance to be proud of,” he told the post-match press conference.
Ronaldo Joybera Junior and substitute Hadi Fayyadh Razak scored for Indonesia and Malaysia respectively during the match.
However, in the shootout, Indonesian goalkeeper Ernando Ari Sutaryadi emerged the hero after saving attempts from Hadi and Luqman Hakim Shamsudin.
Indonesia also missed one when Asnawi Mangkualam Bahar hit the bar.
This was the second consecutive loss for Maloney’s charges in this edition of the biennial games after their heartbreaking semifinal defeat in extra-time against Vietnam on Thursday.
Despite returning home empty-handed, Maloney was proud of the commitment and spirit shown by his squad.
“It’s disappointing not to bring home a medal but I can’t fault the boys’ performance. These players, I believe, performed beyond expectations and they competed with nations with overaged players. I couldn’t give them enough credit,” he said.
Maloney said the focus after this will be on the U-23 Asian Cup Championship in Uzbekistan from June 1 to June 19 which will see Malaysia once again play Vietnam and Thailand, as well as giants South Korea.
The 50-year-old Australian said the experience of going through six matches in 14 days in Hanoi could come in handy against tougher competition in Uzbekistan.
“It’s over now so we have to put it behind us and refocus on the next tournament, we do meet Vietnam and Thailand in the Asian Cup tournament group stage so we’ll face them again and we should be well prepared for that and take a lot out of this tournament (SEA Games),” he said.
The defeat yesterday meant that the national squad failed to pick up a medal at the SEA Games for the second consecutive time after Ong Kim Swee’s squad took silver in 2017.