The Portuguese international was among the goals as Erik ten Hag’s sealed a top-four finish by beating Chelsea 4-1 at Old Trafford on Thursday night.
Casemiro and Anthony Martial scored in the first-half before Fernandes won and scored a penalty and Marcus Rashford got on the scoresheet after the break.
While it was always unlikely Liverpool would be able to catch the Red Devils on the final day, the three points make it mathematically impossible.
Reds forward Mohamed Salah vented his frustration after watching United follow Newcastle in making it into Europe’s elite club competition, admitting he was “totally devastated.”
“We know it means a lot [to the fans],” Fernandes told Sky Sports.
“For us it’s about getting our goals. We know we’d be happy also for Liverpool to not be there but for us it’s about getting the best for ourselves.”
It is the first time Jurgen Klopp’s side have played in Europe’s secondary club competition since his first few months at the club in the 2015/16.
United could yet spoil another rival’s season when they meet Manchester City in the FA Cup final next month as Pep Guardiola’s side chase what could be a treble.