Background: We aimed to investigate the accuracy of salivary matrix metalloproteinases (MMP)-8 and -9, and tissue inhibitor of metalloproteinase (TIMP)-1 in diagnosing periodontitis and in distinguishing periodontitis stages (S)1 to S3. Methods: This study was a case–control study that included patients with periodontitis S1 to S3 and subjects with healthy periodontia (controls). Saliva was collected, and then, clinical parameters were recorded, including plaque index, bleeding on probing, probing pocket depth, and clinical attachment level. Diagnosis was confirmed by assessing the alveolar bone level using radiography. Salivary biomarkers were assayed using an enzyme-linked immunosorbent assay. Results: A total of 45 patients (15 for each stage) and 18 healthy subjects as controls were included. The levels of all salivary biomarkers and clinical parameters were significantly higher in periodontitis subjects than in the controls. The ROC curve showed that MMP-8, MMP-9, TIMP-1, MMP-8/TIMP-1, and MMP-9/TIMP-1 had statistically significant diagnostic accuracy, with areas under the curve (AUCs) of 0.892, 0.844, 0.920, 0.986, and 1.000, respectively, when distinguishing periodontitis from the controls. Similarly, these biomarkers showed significant diagnostic accuracy in the differentiation of S1 periodontitis from the controls (AUC range from 0.902 to 1.000). Conclusions: This study suggested that salivary biomarkers exhibited high diagnostic accuracy in distinguishing periodontal health from periodontitis in general as well as S1 periodontitis. Furthermore, TIMP-1 could differentiate S1 from S3.