Alaves squandered a number of chances before Barcelona broke the deadlock in the 87th minute when De Jong latched on to a Ferran Torres pass to fire in from close range.
Barcelona, who have already been eliminated from this season’s Champions League and Copa del Rey, climbed to fifth in the standings with 35 points from 21 matches. They trail leaders Real Madrid by 15 points, with a game in hand, and are only a point adrift of fourth-placed Atletico Madrid.
“The victory was really important because of our situation in the league and the difficult season that we are going through, but we still have a lot of things to work on and improve,” de Jong told reporters.
It was a lacklustre and flat game at Mendizorrotza Stadium, with players complaining about the frozen pitch.
Barca tried to shake things up after the break with the introduction of 20-year-old midfielder Nico, while Gerard Pique’s close range shot was blocked thanks to a brilliant left-footed save from Fernando Pacheco.
Alaves’ Joselu went close with a powerful header but that flew just wide of Marc-Andre Ter Stegen’s right post.
It was De Jong’s last-gasp effort that finally swung the game Barcelona’s way.
Alaves remained in 19th place with 17 points from 22 games, three points adrift of the safety zone.