Young Boys, who last won the title in 1986, were also left to contemplate the runners-up spot for the third season running while Basel completed a league and cup double in their first season under German coach Thorsten Fink.
Basel went top on goal difference last Thursday after Young Boys slumped to a 5-1 defeat at FC Luzern and, with the fixture list throwing the pair together in the final match of the season, Basel needed only a draw at the Stade de Suisse.
Basel, who finished with 80 points from 36 games, looked more confident and went ahead in the 39th minute when Valentin Stocker, left unmarked, ran on to a long diagonal pass from Carlitos and cleverly flicked the ball over Marcos Woelfi.
Scott Chipperfield headed the second in the 61st minute from Stocker's cross, although the Australia midfielder was lucky to escape injury when he failed to clear an advertising board in his celebration and fell flat on his face.
Young Boys' frustration boiled over and Stocker, picked for Switzerland's World Cup squad, was stretchered off after being hacked down.
Young Boys had Xavier Hochstrasser sent off for a late tackle on Beg Ferati in a niggly finale to the match.
Apart from one week in March when Basel went top, Young Boys led from the third match day last July and at one point were 10 points ahead of Basel.
Young Boys forward Seydou Doumbia finished as top scorer with 30 goals.
