Jordan were playing in their first Asian Cup final and seeking their first major trophy, but it was Qatar who prevailed in front of 86,492 fans including Qatar's ruler Sheikh Tamim bin Hamad al-Thani and FIFA president Gianni Infantino.
Yazan Al-Naimat had briefly given Jordan hope when he netted an equaliser in the second half but their dreams were shattered when they conceded two more penalties, put away by Afif who finished as the tournament's top scorer with eight goals.
Afif, who was thrown into the air repeatedly by his teammates after the final whistle, also picked up the award for the most valuable player of the tournament.
Qatar took the lead when Afif won a penalty in the 20th minute as he tried to skip past Abdallah Nasib, with the referee immediately pointing to the spot as Jordan coach Hussein Ammouta reacted furiously on the touchline.
Qatar skipper Hassan Al-Haydos hovered near the penalty spot but once Jordan's players were out of the way, he handed the ball to Afif and the forward stepped up to find the bottom corner from the spot.
The goal was the first Jordan had conceded since their dramatic last-16 win over Iraq and Afif celebrated his strike by performing a card trick for the cameras.
But Jordan switched gears in the second half and pegged Qatar back as they began to find space in behind the defence.
Yazan Al-Arab nearly equalised with a sensational volley from a corner that was hit straight at the keeper while a back-heeled effort at the near post from Ali Olwan moments later went inches wide.
Jordan finally found the equaliser midway through the second half when Al-Naimat controlled a cross with a sublime first touch, escaping his marker to fire home an uncontested shot for his fourth of the tournament.
Parity lasted only six minutes, however, as Qatar won another penalty after a VAR check for a trip by Mahmoud Al-Mardi and Afif made no mistake from the spot.
With 13 minutes added on, Jordan tried their best to find an equaliser once again but Qatar won a third penalty in stoppage time when Afif was through on goal and brought down by goalkeeper Yazid Abu Layla.
The forward kept his composure and stepped up one last time to put the game out of reach for Jordan as the home fans in the stadium erupted and unfurled a huge banner which featured their heroes from 2019 and the words "2023 loading".
