Rooney's goals helped United to a 4-0 win at Club Brugge, sealing a 7-1 aggregate win over the Belgian side in the final qualifying round.
The England captain had not scored for the Red Devils since April, a run of 10 games and 878 minutes and his early season performances in the EPL had attracted some criticism.
But after United survived some early home pressure, his first goal on 20 minutes, assisted by Memphis Depay, effectively ended the tie as a contest.
Rooney's delicate finish over home goalkeeper Sinan Bolat was followed by two further strikes after the break as United took command.
It was his first United hat-trick since 2011 and took his tally for the English powerhouse to 233 career goals.
Ander Herrera, who had set up Rooney for his second, completed the scoring.
Mexico's Javier Hernandez should have added a fifth, but he missed a penalty and spurned a late easy chance in front of goal.
But that will matter little to Louis van Gaal's men, who will go into the group stages of the Champions League for the 20th time, having failed to qualify for last season's competition.
Elsewhere, Bayer Leverkusen beat Lazio of Rome 3-0 to go through 3-1 on aggregate, while CSKA Moscow saw off Sporting Lisbon 3-1 to give the Portuguese side a 6-3 win on aggregate.
Astana is the first Kazakh side to reach the group stages as a late Nemanja Maksimovic goal helped it edge Apoel Nicosia.
Belarus will be represented by BATE Borisov, who put out Partizan Belgrade.