Maulana Egy Vikri opened the scoring for Indonesia after just four minutes and Ardiles Haay finished off the three-time defending champions four minutes from time in a Group B match.
The other teams in the group are Vietnam, Singapore, Laos and Brunei.
Group A comprises the Philippines, Malaysia, Myanmar, Cambodia and Timor Leste.
The top two teams in each group advance to the semi-finals of the 30th edition of the biennial event which officially begins on Saturday and ends on Dec 11.
"Indonesia were well prepared and did well. We conceded the first goal early because we lost our concentration," Nishino said after yesterday's match.
"The result certainly was not good for us. We have to accept it. Our players gave their all.
"We now have to check our players' fitness levels as some of them looked exhausted in the final stages of the match."
Nishino refused to use the artificial pitch at Manila's Rizal Memorial Stadium as an excuse for the loss.
"It may affect our team. But we were not the only team on the pitch -- Indonesia also played on the same pitch. It was the Indonesians who adjusted themselves to it better than our players," said the Japanese, who also oversees Thailand's senior team.
According to the rules, each team can have two overage players but Nishino did not pick even one.
Asked if this puts Thailand at a disadvantage, Nishino said: "Having overage players may be an advantage.
"But I believe that our players are capable of competing against any teams, including those who use overage players. We must have faith in our players."
In Tuesday's action, Nishino left forward Supachok Sarachat on the bench and filled teenager Suphanat Mueanta in the starting line-up.
Indonesia got off to a fast start when Vikri put the Garudas ahead in the fourth minute.
Vikri's first attempt was saved by Thailand goalkeeper Nont Muangngam but he was helpless as the starlet poked in on the rebound.
As Thailand threw everything at the Indonesians in an attempt to get an equaliser, the War Elephants were punished in the 86th minute when Haay went clear on the break and beat Nont.
"We have Peerawat Akkrathum with the team now as a replacement for [injured] Ekanit Panya, but Worachit Kanitsribumpen has become a doubtful starter for the match against Indonesia, weakening our midfield.
"I have talked to the players about our attacking and defending strategies, but today we focused on the artificial pitch in training.
"There are several things that I am quite worried about apart from the pitch surface. I can only tell the players and the staff coaches to do their best while on the pitch."
Nishino added that he had yet to see the Indonesian U23 squad in action.
"I have only seen some brief videos of their recent games, but I am confident that we will pick up three points from our first game."
Earlier, Indonesia coach Indra Sjafri said: "We are here with high hopes. We have won this tournament once in 1991, so we can do it again."
Meanwhile, Ha Duc Chinh scored four times as Park Hang-Seo's Vietnam began their campaign with a 6-0 rout of Brunei at Binan Football Stadium.
Finding themselves in a group featuring defending champions Thailand, Indonesia, Singapore, Laos and Brunei, Vietnam knew they had to get their campaign off to a good start and that was what exactly they went and did at Binan in their opener.
Brunei's marking from set pieces left a lot to be desired for and Duc Chinh took full advantage to net four goals, playing the starring role for Vietnam.