In a combined event with the Czech Republic, prolific sprinter Sagan raced to a solo victory, crossing the finish line 35 seconds ahead of Czech riders Michael Kukrle and Dominik Neuman.
Peter's win makes it 11 years of Sagan dominance in the event with brother Juraj having won four times including last year, but he was unable to compete in 2021 due to a broken collarbone.
"I'm very proud and happy to have won my seventh Slovak national championship," Sagan said following the race.
"I'd like to thank everybody for their support during the race, it feels nice to be back in Slovakia."
Sagan's BORA-Hansgrohe teammates made it a hat-trick of national titles, with Max Schachmann taking out the German prize and Patrick Konrad soloing to victory in the Austrian race.
Elsewhere, Wout Van Aert (Jumbo-Visma) won his maiden Belgian road race title after besting Edward Theuns (Trek-Segafredo) and Remco Evenepoel (Deceuninck-Quickstep) in the final sprint.
Seemingly hitting form at the right time heading into Le Tour with a victory at the Amstel Gold in April also under his belt, Van Aert admitted he still believes there's room to grow.
"It's one of the most beautiful jerseys in the peloton," Van Aert said. "Obviously I wanted to win it one day.
"It sounds ridiculous after a victory but there's certainly room for improvement. Today I had to undergo the race and bide my time.
"I rode several championships where it didn't work out well. Today I managed to get into the right breakaway move.
"Due to circumstances this is a very pleasing victory. The Tour de France is very different to this race but I had doubts and now I can head to the Tour with confidence and show the tricolour jersey."
2020 Tour de France champion Tadej Pogačar (UAE Emirates) finished fifth in the Slovenian national road race, 1 minute and 44 seconds behind winner Matej Mohorič (Bahrain-Victorious).