Miguel Flano had given the hosts the lead in the first half after shocking marking from the visitors had allowed him a free header from Alvaro Cejudo's corner.
However Betis were by far they better side after the break. Osasuna keeper Andres Fernandez made great saves to deny Roque Santa Cruz and Ruben Castro while Lolo cleared a goalbound effort off the line.
The visitors did eventually level when Castro stayed just onside the turn in Jonathan Perreira's cross with 10 minutes remaining.
Betis continued to push on in an attempt to win the game but after Castro had hit the bar and Fernandez again denied Santa Cruz, Osasuna stole all three points with the last kick of the game as Nekounam curled a free-kick into the top corner from 20 yards.
Pepe Mel had admitted prior to the match that he would almost certainly lose his job should Betis go a 10th league game without a win, but he certainly could not be accused of having lost the faith of his players as they bossed an Osasuna side that still haven't been beaten at home this season for the majority of the match.
Osasuna - Real Betis 2:1 by FootballKing1892