The SARS-CoV-2 outbreak has provoked more than 6 million deaths worldwide. The scarcity of effective treatments and its virulence converted the vaccines into an essential tool to face it. The most used vaccines were the mRNA, adenovirus vector, and inactivated whole-virus. However, nowadays, infants aged < 6 months are not eligible for any vaccines against COVID-19, and their immunization relies on the passive immunity. In this research, we investigated the humoral and cellular immune response generated on newborns of SARS-CoV-2 vaccinated mothers with mRNA or viral vector (VV) vaccine employing Fourier transformed infrared (FTIR) spectroscopy in saliva samples. For this purpose, saliva samples of newborns and their mothers were collected; the population was divided in two groups, VV and mRNA, which were subdivided into three subgroups: before pregnancy (BP), at the first (FTP) and second (STP) trimesters of pregnancy. The samples were analyzed using FTIR spectroscopy, and the bands associated to the humoral and cellular immune responses, such as IgG, IgA, and IFN-γ were analyzed. To elucidate the quantity of those immunoglobins and the cytokine, the integrated areas were calculated and compared. Likewise, the correlation of the humoral and cellular immune response between the newborns and their mothers was also evaluated, as well as the correlation between cellular and humoral immune response. Compared with the mRNA vaccine, the VV vaccine produced a significant humoral and cellular immune response in newborns and their mothers when they received it at the STP. However, no correlation was observed between newborns and their mothers. The mRNA vaccine showed a more significant humoral immunity generation in newborns and their mothers when it was administrated BP. Nevertheless, compared with the VV vaccine, it only showed statistical significance in the mothers, highlighting that IgG showed a moderate positive correlation between the newborns and their mothers.