On an evening of high drama in the last round of matches this season, eight games kicked off at the same time with three European places and two relegation slots at stake.
Malaga climbed to 58 points, ahead of Atletico Madrid and Levante who finished fifth and sixth respectively to secure entry to the Europa League.
Europa League winners Atletico beat Villarreal 1-0 and condemned the team that finished fourth last season to relegation along with Sporting and Racing Santander.
After Malaga defender Martin Demichelis had hit the post midway through the first half of a tight encounter at La Rosaleda, Venezuela striker Rondon's header three minutes after the restart sent the Andalucian side into the Champions League for the first time.
The goal was his 11th in the league this season, confirming him as the club's top scorer in the process.
Abdelkader Ghezzal's brace had spend-thrift Levante on course for a fifth-place finish for much of the evening, only for Radamel Falcao's 24th goal of the season in the 88th minute to grab a dramatic 1-0 win for Atletico at Villarreal which moved the Europa League holders fifth, bumped Levante down to sixth and sent their hosts down into the second tier.
Javier Farinos scored a third for Levante against Athletic Bilbao from the penalty spot, though it served as little more than to be one more cause for celebration at the end of an incredibly high-achieving season for the Valencia club.