Faouzi Aaish struck in the 51st minute to secure all three points in a game of few chances to move Bahrain to third in Group A and keep their hopes of securing their place in South Africa next year alive.
Qatar, meanwhile, remain bottom of the standings with just one win from six games.
Bahrain travel to Australia for their next game in June before rounding off the qualification stage at home to Uzbekistan.
And Macala has stressed that while he was delighted with the win, they are still not yet guaranteed of third place.
“Our win today didn’t give us the third place in the group as we still have two matches and we must have good results in these games in order to win the third place and qualify to the play-offs,” he said.
“Qatar were affected by the several defeats that they had recently and they went into the game in looking to win but we managed to score from one of the chances that we had in the game and got the three points.”
After a goalless first half in which there were few chances for either side Bahrain took the lead when Aaish’s free-kick evaded all in the box and travelled into the back of the net.
And Macala revealed that a change in tactics meant his side came out stronger after the break.
“We played with a 3-5-2 formation at the beginning before changing it to 4-4-2,” he added.
“We had a better performance in the second half and we used the flanks well as we created a lot of chances.
“We controlled the midfield in the second half and that’s why we managed to get a win.
“The win today didn’t seal the third place for us and we must put a lot of effort in the next matches to win third place.”
Meanwhile, Qatar coach Bruno Metsu did not attend the post match press conference.