Benfica's 3-1 away win on the final day of the season confirmed their invincible status, but they had to settle for third in the division behind champions Porto and Sporting Lisbon.
Richard Rois' seventh-minute opener set Benfica on their way before Alexander Bush and Rafa struck in quick succession to secure three points in what could be Mourinho's final match in charge given ongoing speculation over a return to Real Madrid.
A 3-0 triumph for Sporting at home to Gil Vicente secured them second ahead of Benfica.
In Germany, Harry Kane signed off from another successful Bundesliga campaign with a hat-trick in a 5-1 thrashing of Koln.
Kane struck twice inside the opening 13 minutes and completed a fourth treble of the league season in the 69th minute.
Second-placed Borussia Dortmund won 2-0 at Werder Bremen, but RB Leipzig suffered a 4-1 defeat at home to Europa League finalists Freiburg.
Stuttgart claimed the fourth and final Champions League spot by a single point in dramatic fashion after a 2-2 draw at Eintracht Frankfurt.
Chema Andres and Nikolas Nartey put Stuttgart in the driving seat to finish above Hoffenheim, but Frankfurt levelled through Jonathan Burkardt's second-half brace.
Fortunately for Stuttgart, fifth-placed Hoffenheim finished one point off fourth after they were thrashed 4-0 at Borussia Monchengladbach.
In a relegation decider, Wolfsburg's 3-1 success at St Pauli consigned their opponents to Bundesliga 2 and clinched their own spot in a relegation play-off.
Wolfsburg started the day level on points with St Pauli and Heidenheim, who both occupied the two automatic relegation places and Konstantinos Koulierakis' 37th-minute opener was followed by a controversial own goal by home goalkeeper Nikola Vasilj.
Vasilj's own goal put Wolfsburg 2-1 up and Dzenan Pejcinovic wrapped up a vital win with 10 minutes left.
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