Swallows started the game off well, and 'Dube Birds' marksman Alton Meiring had a great chance to put his side in front in the 17th minute, but having been set up by Tsweu Mokoro and only 15 yards out from goal, he ballooned his shot over the bar.
At the other end of the field, a quick one-two saw Eleazar Rodgers bursting through on goal, but his shot was well saved by Birds custodian Greg Etafia.
Swallows midfielder Sibusiso Themba had a free-kick go over the bar after 27 minutes as the 'Beautiful Birds' continue to pile the pressure on the visitors.
'The People's Team' took the lead three minutes later when Edwin Isaacs converted from the spot after Bevan Fransman was adjudged to have fouled Thom-Rick October inside the box.
The score remained 1-0 in favour of Santos at half-time.
The second half saw Santos quickly on the offensive and Etafia again came to Swallows' rescue when he saved from Rodgers.
However, there was nothing he could do to stop Santos from doubling their lead in the 51st minute when Mogogi Gabonamong hammered in a low shot from inside the big box.
Swallows gave themselves brief hope in the 61st minute when top PSL goal-scorer James Chamanga headed home a cross by Sibusiso Themba to take his goal tally to 11 for the 2007/08 season.
However, the Cape Town side proved to be stronger in the latter stages of the game and added two more goals to seal the win.
Swallows are now ninth in the Premiership standings with 22 points and will want to resume their winning ways when they clash with Golden Arrows on Saturday, February 23.
Swallows v Thanda
Venue: Olen Park
Swallows v African Warriors
Venue: Germiston Stadium
Cosmos v Swallows
Venue: Mehlareng Stadium
Won 3-1 v Leopards
Venue: Thohoyandou Stadium
Won 3-1 v Celtic
Venue: Johannesburg Stadium
Won 3-1 v Sundowns
Venue: Loftus Stadium
Lost 0-1 v Arrows
Venue: King Zwelithini