Hojlund replaced Marcus Rashford in the 56th and scored an equalizer six minutes later after Amad Diallo's shot was deflected by goalkeeper Martin Jedlička into his path for an easy finish.
The 21-year-old Hojlund also scored twice in the previous round, when United beat Norwegian team Bodø/Glimt 3-2, and has five goals in his six appearances in the second-tier competition.
“It feels good to have scored two goals but I am more happy with the win,” Hojlund said. "My instructions? Go out there and score two goals! Just to use my qualities, run the channels and be assertive in front of goal.”
United had come off two straight losses in the English Premier League, 2-0 away to Arsenal, and 3-2 at Old Trafford to Nottingham Forest that left the club 13th and eight points adrift of the top four as progress looked slow under new coach Ruben Amorim.
Ahead of the late games, United moved to fifth place in the Europa League. It has 12 points from six games after three wins and three draws.
Matěj Vydra, who previously played for Burnley and Watford, opened the scoring three minutes into the second half.
Among other early results, substitute Sergio Peña equalized in stoppage time for Malmö to hold unbeaten Galatasaray 2-2, and PAOK routed Ferencvaros 5-0.
Roma showed signs of improvement by beating Braga 3-0 for a second straight victory that came after the struggling club earned its first win under new coach Claudio Ranieri, 4-1 over visiting Lecce in Serie A.
Braga goalkeeper Matheus received a red card in the 68th when his team was losing 2-0.
Among other games later Thursday, Rangers host Tottenham.
Conference League
A youthful Chelsea lineup made the most of a long trip to Kazakhstan by beating Astana 3-1 on Thursday to stay perfect in the UEFA Conference League.
Marc Guiu struck twice within five minutes early in the first half. The 18-year-old forward opened the scoring on a solo effort in the 14th and added his second after meeting a cross from Pedro Neto from the right in freezing conditions in the Kazakh capital.
Guiu, who joined Chelsea from Barcelona this summer, has scored three in the competition.
Renato Veiga, who is 21, headed home the third off a corner before Marin Tomasov scored for the hosts late in the first half.
Neto was the only player to remain from the squad that beat Tottenham 4-3 on Sunday to move to second in the Premier League.
Chelsea has 15 points atop the standings of third-tier competition with one more game to play in the league phase.
Fiorentina crushed LASK 7-0 and Legia Warsaw lost 2-1 at home to Lugano.
In another early game, Swedish team Djurgarden beat Vikingur 2-1 in Iceland.
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