Perez hit three as the Gunners wrapped up a comprehensive 4-1 victory in Switerzland, with Alex Iwobi adding the fourth and Seydou Doumbia grabbing a late consolation for the hosts.
The win, coupled with Paris St Germain only scraping a draw against minnows Ludogorets, means Arsenal advance to the first knockout round as group winners for the first time since 2012.
Currently Benfica, Bayern Munich and Bayer Leverkusen are the three definite sides than can be paired with Arsenal in Monday's draw in Nyon as they have progressed as runners-up.
But one of either Borussia Dortmund or Real Madrid will also be added to the equation after Wednesday's matches - as will Juventus or Sevilla, who are still fighting for top spot in Group H.
Wenger's side have fallen at the round of 16 stage in the last six seasons but, despite progressing as the best in Group A, he is taking nothing for granted this year either.
“I don't even know who we can get,” he said after the win.
“But we can still have a difficult draw, as I said last night. Any way, it will be difficult but with less guilt when you finish first.
“You feel you've done the job and can play the second leg at home. So we have achieved that. But the draw is not much different (in terms of the potential opponent), certainly at the moment.
“I cannot complain tonight. I've had bad nights in football and tonight was a good night. Overall we came here wanting to do the job, wanting to play well.
“On top of that we were lucky with the result with Paris St Germain, so it was a positive night.”
Wenger opted to take a strong squad to Switzerland and he played Alexis Sanchez and Mesut Ozil from the start.
Both played their parts in setting up Perez's first two goals, with the Spaniard tapping home to open the scoring from Kieran Gibbs' cross and then again when the same player's shot was palmed into this path.
He completed his hat-trick just after the interval with a well-taken strike before Ozil squared for Iwobi to wrap up the win.
Sanchez and Ozil were then taken off and wrapped in cotton wool ahead of a busy schedule, and Wenger was pleased his decision to stick with a strong side rather than shuffle his pack was vindicated.
Asked if his brave team selection paid off, he replied: “Yes, I feel we had a good start, we were quite mobile and technically very agile as well, and quick.
“Overall the speed of our start surprised Basle. It was a convincing performance tonight. Since the start of the season our squad system has worked well.”
The Frenchman was also full of praise for Perez, starting just his fifth game since his summer move from Deportivo La Coruna.
He had only scored an EFL Cup brace against Nottingham Forest before this hat-trick but Wenger insists there is more to come from the 28-year-old forward.
“The first two looked easy goals, created by the team to make, what you call in England, tap-ins,” he added.
“But he is there. You have to be there. The third was a real striker's goal. He scored over 20 goals in Spain last year, and showed tonight why.
“He has a good eye and makes good movement in the box, and that's why he scores.”
Original source: Wenger expects tough Champions League draw