By Gabriel Tan in Bangkok
The War Elephants, who are looking to win the competition for a record fourth time, started the match in dominant style and claimed a two-goal lead at the break thanks to strikers from Jakkapan Pornsai and Anucha Kitpongsri.
However, their failure to convert their possession into goals nearly came back to bite them in the 77th minute when Paul Mulders pulled one back for the Azkals, although Thailand ultimately held on for all three points.
And while the majority of their display exemplified why many regard them as title favourites, Schafer insists things were far from smooth-sailing.
"It was a very difficult match today [Saturday]," he said at the post-match press conference. "Philippines have very strong players with very good fitness.
"In the first half, it took us 20 minutes before we created our first chance.
"In the second half after 50 minutes, we did not concentrate and started losing the ball. This allowed Philippines back in the game, which is not good.
"We played against what I would call a 'European' team, with almost all of their players hailing from Europe. But that's not my problem.
"Congratulations to my team, who played very well. Our first goal was fantastic and we only made one mistake in the game, which led to Philippines scoring."
Thailand can now secure their progress to the semi-finals with a win over Myanmar on Tuesday, but after seeing Park Sung-hwa's men hold Vietnam to a 1-1 draw earlier on Saturday, Schafer admits his side cannot afford to take them lightly.
"I'm expecting a very difficult match against Myanmar," the German added. "Myanmar have many good players.
"We will need the same as today [Saturday] - 100%."
Philippines coach Michael Weiss, who spent the final nine minutes of the game watching from the stands after being sent off by referee Sato Ryuji for throwing the ball at a fallen opposition player, defended his actions, which infuriated the Thai camp.
"I had no intention to hit the player," he explained. "All I did was throw the ball and it happened to hit the player, then there was a lot of commotion and the referee gave me a card.
"I speak a little Japanese and I criticised him and maybe he didn't like that but I want to say the referee isn't the reason why we lost the game."
Weiss was nonetheless keen on congratulating Thailand for what he felt was a deserved victory, but lamented his side's lack of composure, which resulted in them lofting aimless balls into the final third.
"Congratulations to Thailand for this 2-1 win," he added. "Overall, it was deserved.
"We had a good start in the first 15 to 20 minutes but then Thailand got aggressive and broke down our unit. We couldn't build up well from behind and relied mostly on long balls, which is not what we wanted.
"We couldn't keep our concentration for a five-minute spell and the game was decided."
The 47-year-old did ring the changes by replacing Emelio Caligdong, Phil Younghusband and James Younghusband with Jeffrey Christiaens, Marwin Angeles and Patrick Reichelt respectively, and believes the substitutes did well to get his side back into the game.
"I tried to make a couple of changes which paid off," Weiss explained. "We didn't let them come into the game in the second half.
"All three players played quite well and there was better balance with Marwin in midfield. We need players who are 100% fit."
Philippines will be looking to pick up their first points in the group on Tuesday when they take on Vietnam.
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