The Netherlands striker scored just in time to defuse a Villarreal comeback and secure Barcelona's 3-1 victory on Saturday, and end his team's winless record in the Spanish league La Liga.
David de Gea made two crucial saves and United, with Michael Carrick in caretaker charge, took advantage through Ronaldo's 78th-minute lob.
Emery said he was grateful for being considered for the Newcastle job but was “even more grateful” for being able to continue with the Spanish club.
Gerard Moreno is also the first player to score 30+ goals for Villarreal in a single season in all competitions since Giuseppe Rossi.
Hakim Ziyech had a bittersweet evening as he continued his fine pre-season form into competitive action with the opening goal.
Villarreal clinched the title with a victory over Manchester United in a penalty shootout on Wednesday in Poland.
Europa League final: We didn't play as well as we know we can, laments Manchester United coach Solskjaer
Manchester United goalkeeper David de Gea ended up missing the decisive penalty in the shootout and this gave Villarreal a famous victory in the final.
For Villarreal coach Unai Emery it was a record fourth Europa League title, and it offered a measure of redemption after he was fired by Arsenal last season.
Up to 30 attackers may have been involved, Gdansk police spokesman Michal Sienkiewicz told Polish broadcaster TVN24 on Wednesday.
Sergio Ramos will be back in the squad after recovering from an injury that has kept him out since March.
Atletico leads defending champion Real Madrid by two points with two matches remaining and will win the title if it beats Osasuna at home and Madrid fails to win at Athletic Bilbao.
There is no fracture, hopefully Harry Maguire will be ready for Europa League final: Manchester United gaffer Ole Gunnar Solskjaer
Manchester United skipper Harry Maguire is now racing time to be fit for Europa League final date against Villarreal on May 26.
Sevilla produced their second stunning comeback in five days by overcoming a 2-0 half-time deficit to win 3-2 at Villarreal on Sunday.
Ex-Tottenham striker Roberto Soldado is set to join Turkish Super Lig side Fenerbahce after two seasons at Villarreal.