Scotland took the lead after just three minutes through Lee Erwin and Islam Feruz doubled the score early in the second half when he converted a penalty.
Another friendly match between the two teams will be played on Wednesday at 18:30.
MALTA: Carlos Dimech, Sacha Borg, Christian Grech, Keith Tanti, John Debono, Ayrton Azzopardi, Lee Galea, Michael Camilleri, Ryan Scicluna, Bjorn Kristensen, Larson Mallia.
Subs: Karl Magri, Steve Agius, Zach Muscat, Ian Xuereb, Ryan Dalli, Dylan Micallef, Matteo Desira Buttigieg.