The current study aimed to investigate the prevalence and molecular characterization of biofilm-positive S. aureus isolates from bovine subclinical mastitis. The study also highlights the role of commonly used NSAIDs and ivermectin to modulate the S. aureus-associated antibiotic resistance. The results found a 41.41% S. aureus prevalence, out of which 25.79% isolates were biofilm-positive based on Congo red agar, microtitre plate test, and presence of icaA gene. Phylogenetic analysis of study isolates showed a high similarity with Egyptian and Indian icaA-positive S. aureus isolates. The comparative antibiotic resistance profiling showed a significantly (p<0.05) higher resistance to gentamicin, oxytetracycline, and cotrimoxazole by biofilm-positive isolates compared to non-biofilm forming isolates. The prevalence of methicillin and vancomycin resistant S. aureus was 62.5 and 20.83%, respectively. Antimicrobial effects of non-antibiotics against study isolates accessed through well diffusion method showed higher zones of inhibition for meloxicam followed by flunixin, ketoprofen, and ivermectin. The combinations of resistant antibiotics with non-antibiotics were investigated using well diffusion method and checkerboard assay. The combinations of amoxicillin/meloxicam, cotrimoxazole/flunixin, cotrimoxazole/ ketoprofen, and gentamicin/flunixin on well diffusion method and cotrimoxazole/ flunixin, amoxicillin/ketoprofen and gentamicin/flunixin on checkerboard assay revealed synergistic interactions. The study concluded that biofilm positive S. aureus is an emerging and prevailing cause of bovine mastitis in dairy farms of Pakistan. The increasing antibiotic resistance in S. aureus can be modulated by combining the resistant antibiotics with NSAIDs, especially flunixin and ketoprofen.