A Divock Origi goal in the 88th minute gave the Belgians the three points and qualification to the last 16 and left Capello's team with a solitary point ahead of their final Group H game against Algeria.
"To be honest, I am very happy with the performance of the team, the result isn’t fair but the reality is that we lost," Capello told a news conference.
"We had the chances to win, it was a nice game with both teams trying to win unfortunately they were the ones able to do it," added the Italian coach.
Belgium were on top for the opening 45 minutes but Capello said his team had opportunities to win the game that they failed to make the most of.
"We played a large part of the first half on the counter-attack and we had chances, but we made mistakes with the final pass and maybe we also shot a little to hurriedly.
"But in the second half – the team was almost bossing the game, the reality is that when Belgium go forward on the break they are very dangerous," he said.
Capello said his decision to bring on Alan Dzagoev in place of Oleg Shatov with seven minutes remaining was aimed at trying to get a late winner.
"When I put in Dzagoev I was looking for us to win the game. We were playing close to their area and I thought he could make the final pass. But we conceded to a counter-attack. That was not Dzagoev’s fault – it was because we were trying to win," he said.
The Brazilian crowd had expressed displeasure with the quality of the game, which was generally disappointing, but Capello said he thought such criticism was unfair.
"I think it was an excellent game, played at a great rhythm, great intensity. Maybe because of that intensity we made mistakes and so did they. I think it was an intense and interesting game," he said.
Algeria play South Korea later on Sunday but Capello knows his team needs to win their final game to have any chance of progressing.
"There is only once chance against Algeria – a draw solves nothing," he said, adding that he remained sure his team could make it to the last 16 even if the tournament was part of a learning curve.
“I still believe (we can qualify), absolutely I believe. The important thing, as I said when we came to play this World Cup after 12 years away, this is needed in order to understand the level that we have to confront when you are in competitions like this," he said.