Afif on Sunday described his transfer as a "dream" after his move was confirmed by his parent club Al Sadd and the Spaniards.
"It is a dream come true for me to be the first Qatari player in La Liga," Afif said in an interview with the Supreme Committee for Delivery and Legacy, the body organising the Qatar 2022 World Cup.
"I am very happy to sign for Villarreal, they are a big team and one of the best teams in Spain."
He added that he would aim for the first team next season.
"Villarreal will play the Champions League next season so we’ll try to be a difficult team to beat in La Liga and go as far as we can in all competitions," said the young history-maker.
Al Sadd, the Doha club for which Barcelona great Xavi Hernandez now plays, took to social media on Saturday evening to say it had reached a deal with Villarreal.
And in a statement on its website, subsequently retweeted by Afif, Villarreal also confirmed that an agreement had been reached "in principle".
The 19-year-old, born in Doha, is no stranger to Spanish football having played for Villarreal and Sevilla's youth teams.
Since 2015, Afif has been playing for KAS Eupen, a Qatari-owned team in the Belgian second division.
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Eupen is owned by Qatar's renowned Aspire Academy, which has spent millions trying to develop young Qatari sports stars over the past decade. Afif is a product of Aspire.
His transfer to arguably the strongest European league could be seen as a major coup for Aspire.
During the current season he scored six times in 16 appearances for Eupen, who subsequently have gained promotion to Belgium's top division.
Eupen director Christoph Henkel said in a statement posted on the club's website that he was sorry to see Afif leave but the club "wished him luck and success in his future career".
A fast and technically proficient player, Afif made his debut for the Qatari national side last year during the country's record 15-0 trouncing of Bhutan in an AFC World Cup qualifier.
He is likely to feature in Qatar's make-or-break matches for the 2018 World Cup in Russia, with qualifiers taking place from later this year.
Villarreal currently lie fourth in La Liga and have already secured qualification for next season's Champions League.
They will be placed in the tournament play-off round before the main group stage.
Several other young Qataris play in Europe, but it is thought that only one other Qatari has appeared in a major league.
Hussein Yasser made one appearance for English club Manchester City in the 2005/6 season.
Yasser was in his early 20s when he made his only appearance during a defeat on penalties to Doncaster Rovers in the League Cup.