The forward, who had only been on the field for seven minutes, forced a superb reaction save from home goalkeeper Roberto in the last seconds of the 90 minutes.
But a dramatic winner at that stage would have been more than a lacklustre game deserved - and also harsh on Zaragoza, who saw a Helder Postiga goal disallowed by a marginal offside call shortly after the hour mark.
Postiga drew a sharp save from Willy Caballero in the early stages with a 20-yard shot before Roberto made a good double save from Ruud van Nistelrooy at the other end.
Eliseu's ambitious long-range effort was deflected wide and, when Joaquin went for goal direct from the corner, Efrain Juarez headed off the line.
Julio Baptista curled a free-kick just wide for Malaga but Zaragoza had the better of what remained of the first half.
Caballero saved from Pablo Barrera and Joaquin blocked Postiga's long-range effort, the Portuguese wasting the ensuing corner.
Postiga lashed a 30-yard shot over the bar before the hosts lost defender David Mateos to injury, Maurizio Lanzaro taking his place.
The second half was even more lacklustre, although Postiga was denied by a marginal offside flag in the 62nd minute.
The same player had a weak low shot easily saved by Caballero before Malaga finally re-emerged as an attacking force in the closing stages.
Santi Cazorla shot over and Sergio Duda's corner was met by Martin Demichelis, but the Argentina defender's header was also too high.
The visitors lost Baptista to injury, Fernandez taking his place - and the newcomer had the best chance of the game as the clock ticked to 90 minutes.
Isco crossed from the right and Fernandez arrived at the far post to meet the ball with a powerful downward header which was brilliantly saved by the diving Roberto.