An 84th minute penalty from Araujo (Clemerson de Araujo Soares) proved the difference at Al Gharafa Stadium in a game the hosts largely dominated but found Pakhtakor keeper Temur Juraev in fine form.
And Caio Junior also underlined a tactical switch that saw Iraq striker Younus Mahmood pushed out to the right flank was crucial to the Qataris’ success.
“My strategy was not to take risks but control the game. It actually happened as we controlled the 90 minutes, but the goal came late. Thank God we scored,” said the Brazilian.
“We played well. Tactically, we were very sound. Putting Younus on the right was the key factor in controlling the game. I am very pleased with such result. It was hard-fought win. We are happy to have qualified for the quarter-finals of the AFC Champions League.
“Playing Younus on the right was a good idea and this helped Clemerson (Araujo), he had plenty of chances to finish the game early.
“Such a move has helped us win matches in the past. We create chances and score and we did that today also.
"As I had expected, the heat affected the players. We played against a very well organised team. That made it very hard for us to score a goal in the first half. I expect that if we had scored in the first half, we would have changed tactics in the second half.”
Caio Junior has now set his sights on going all the way to the final in Tokyo in November.
“I remember that during my first press conference, I said that my dream is to win the AFC Champions League and reach the World Club Championship,” he added.
“It is a big challenge but we have won two championships. The team is at its peak. I am constantly planning for the next stages of this event and I would like to achieve my goals.”
Pakhtakor boss Ravshan Haydarov, meanwhile, felt his side did not get the rub of the green.
"It was an interesting match. Both teams tried to create a good game for the fans. We had chances to score but I feel Al Gharafa were lucky,” he said.
“It was difficult to play in this heat but we have played in such conditions before. I think my players managed well in this heat but it was tough. The penalty was a 50-50 decision. He could have given it or not given it.
“Al Gharafa are a very good team, they have good players. They can do well in the next stages. We could have won this game but we missed four or five players. We played with a lot of young players today."