Qatar topped the group with six points, four points ahead of second-placed China who played out a 0-0 draw with Lebanon earlier on Wednesday.
Tajikistan, meanwhile, received the first red card of the tournament when Amadoni Kamolov was sent off late in the game for violent conduct.
"I'm very pleased to qualify after two matches. It was a difficult match but we prepared really well against a strong team and we didn't give the opponent a chance to score against us," Qatar coach Marquez Lopez told reporters.
"Tajikistan started the match with high pressure, but we were able to handle that."
Tajikistan dominated the opening stages but it was Qatar who took the lead in the 17th minute when Almoez Ali won a scrappy battle in midfield to regain possession and released Afif, who chipped the onrushing goalkeeper to find the net.
"I'd like to send a special message to my wife. Lately I've been playing very well so I'd like to take the opportunity to thank her since I forgot the last time," Afif said with a smile.
Coach Petar Segrt had complaints about the goal as the referee appeared to be involved in a collision with the players in the buildup, but he congratulated Qatar and praised Afif.
"I must accept it. The goal was fantastic, he's a clever player. He was perfect, he had good timing," the Croatian said.
"Qatar's players are strong and clever, but I think also today they were a little lucky... What can I say about the referee, I hope he has a good flight."
Qatar also appealed for a penalty late in the first half when Ali appeared to be fouled off the ball but the referee decided not to award a spot kick after a VAR review, which also saw the two coaches involved in a heated exchange.
Ali nearly doubled Qatar's lead just before halftime when goalkeeper Rustam Yatimov spilled the ball when saving a shot from Afif but Zoir Dzhuraboyev anticipated well to make a crucial block on the goal line.
FULCRUM OF ATTACK
Just as in Qatar's opening win over Lebanon, Afif was the fulcrum of their attack and he continued to torment the Tajikistan defence in the second half.
The 27-year-old created several opportunities with his neat footwork and sharp vision, but his teammates failed to put away their chances.
Tajikistan went down to 10 men in the 81st minute when Kamolov was sent off for kicking Ahmed Al Ganehi in the chin as he fell over while challenging for the ball, with the referee producing a straight red card after a VAR review.
Asian Cup debutants Tajikistan had their moments but they lacked either the final pass or the final touch in the box to test the Qatar keeper, as the central Asian side extended their wait for a first goal in the tournament.
"We had a lot of chances but I can't score the goals myself... I hope we score our first goal in the next game," Segrt said.
