Both Basel and the Swiss League agreed on their respective websites that the team were champions for the third time in a row and the sixth in the last nine seasons.
The confusion over whether or not Basel had won the title capped a chaotic season marred by court battles, hooliganism and financial problems which led to Neuchatel Xamax being kicked out of the league and Servette Geneva filing for bankruptcy.
Basel took an unassailable 16-point lead over FC Luzern last weekend but would not accept the title because their rivals could theoretically have won two points from a case they had taken to the Court of Arbitration for Sport (CAS).
On Saturday, Luzern drew 2-2 with Grasshoppers, meaning they could no longer catch Basel even if they won the CAS case.
However, Basel again refused to celebrate on the grounds that Sion could still catch them should they win an appeal against the Swiss League's decision to deduct 36 points for fielding ineligible players.
The confusion finally ended on Sunday when Basel's win over Lausanne meant they could not be caught even if Sion won back their 36 points.
"Basel are absolutely, absolutely, absolutely, definitively the champions" said the website of 20 Minuten newspaper.
Alexander Frei scored twice taking his tally to 22 for the season and Cameroon forward Jacques Zoua was also on target for FC Basel in stoppage time.
Basel will take part in the qualifying competition for the Champions League next season, Switzerland having lost the right to an automatic place in the group stage.
(Writing by Brian Homewood in Berne; Editing by Dave Thompson)
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