Infestation by Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) causes damage to tomatoes with production losses of up to 100%, affecting the physiological and biochemical aspects of host plants. The objective of this study was to analyze the influence of infestation of cryptic species of B. tabaci MED and MEAM1 on the physiological and biochemical aspects of tomato. Tomato plants ‘Santa Adélia Super’ infested with B. tabaci (MED and MEAM1), and non-infested plants were evaluated for differences in gas exchange, chlorophyll - a fluorescence of photosystem II (PSII), and biochemical factors (total phenols, total flavonoids, superoxide dismutase—SOD, peroxidase—POD, and polyphenol oxidase—PPO). Plants infested with B. tabaci MED showed low rates of CO2 assimilation and stomatal conductance of 55% and 52%, respectively. The instantaneous carboxylation efficiency was reduced by 40% in MED and by 60% in MEAM1 compared to the control. Regarding biochemical aspects, plants infested by MED cryptic species showed high activity of POD and PPO enzymes and total phenol content during the second and third instars when compared to control plants. Our results indicate that B. tabaci MED infestation in tomato plants had a greater influence than B. tabaci MEAM1 infestation on physiological parameters (CO2 assimilation rate (A), stomatal conductance (gs), and apparent carboxylation efficiency (A/Ci)) and caused increased activity of POD and PPO enzymes, indicating plant resistance to attack. In contrast, B. tabaci MEAM1 caused a reduction in POD enzyme activity, favoring offspring performance.