The 19-year-old Isco pounced on a loose ball to open the scoring in the 48th minute at the Sardinero before Alvaro Gonzalez diverted the ball into his own net to make it 2-0 in the 66th.
Manuel Arana pulled a goal back for the home side when he finished off a swift counter-attack four minutes later and substitute Ruud van Nistelrooy crossed for Fernandez (pictured) to volley home with a minute of regular-time remaining.
Malaga have 20 points from 12 matches, two more than their Andalusian rivals Sevilla, who lost 2-1 at home to Athletic Bilbao on Sunday, and three behind fourth-placed Levante, 3-2 losers at Atletico Madrid.
Santander, who have just one win under former Valencia and Inter Milan coach Hector Cuper this season, are on nine points and drop below Real Sociedad to the bottom of the standings on goal difference.
Malaga, on Spain's southern coast, were bought by a member of the Qatar royal family at the end of the 2009/10 campaign and have been busy in the transfer market as they eye a berth in European competition next season.
Managed by former Real Madrid coach Manuel Pellegrini, they landed several high-profile players, including Dutch striker Van Nistelrooy, Spain playmaker Santi Cazorla and French midfielder Jeremy Toulalan.
The table has a familiar look after the weekend action, leaders Real Madrid and second-placed Barcelona having pulled further away at the top thanks to victories over Valencia and Real Zaragoza.
Real edged an entertaining but ill-tempered game at the Mestalla 3-2 for their eighth league win in a row and 11th in all competitions, while champions Barca thumped Zaragoza 4-0 at the Nou Camp, La Liga top scorer Lionel Messi netting his 15th of the campaign.
Real, who host their great rivals in the opening 'Clasico' of the season on December 10, have 31 points, three ahead of Barca. Valencia, the last club apart from the big two to win the title, back in 2004, are third on 24.
