The 27-year-old was hit with the €200 penalty after exceeding the 60km/h (37.2 mph) limit at the Albert Park track on Friday morning.
The Mexican was 1.6km/h over the permitted speed and went on to end the session in a respectable tenth place, six ahead of new teammate Esteban Ocon who was 16th.
Australia, Monaco and Singapore have stricter pit lane rules due to their street circuit status, as the FIA looks to ensure the safety of all involved in the sport. The other 17 tracks on the race calendar have a pit lane speed of 80km/h (49.7 mph).
Ocon joined the team from Manor Racing during the winter break after driving nine races in 2016 for the now-defunct team. The 20-year-old is highly rated within the sport after winning the Formula 3 Championship and GP3 Series in 2014 and 2015, respectively.
Perez was unable to improve his place during his second run and moved down one into 11th although he bettered his time by 0.8s, while Ocon moved up to 13th after cutting 1.6s from his best lap in Practice 1.
The fine comes after both drivers were encouraged to lose weight by the team after it emerged that the 2017 car - which is a bright pink colour - is heavier that expected.
Their disappointing testing in Barcelona raised questions about a team that had ended 2016's Constructors Championship in an impressive fourth place, due in part to Perez' seventh place finish - his best since moving to Formula 1 in 2011.
Most of the drivers on the grid had bulked up to deal with the faster vehicles expected this season but Perez has been forced into an "extreme diet" in order to counteract the heavy structure of his car.
Practice will continue with the third and final session on Saturday ahead of the first qualifying of the race campaign. as predicted current champions, Mercedes, Ferrari and Red bull are leading the way with all those teams occupying the first six places in both sessions.