The Vanarama National League North hosts got off to the ideal start when Connor Oliver found the back of the Boro net only three minutes into the clash at Gateshead International Stadium with a free-kick 20 yards from goal.
Scarborough tried to respond straight from kick-off as midfielder Jordan Deacey took aim just inside the area, but his effort was blocked.
Gateshead could have doubled their lead when Elliot Forbes was given time and space on the edge of the area but he fired wide.
Forbes then robbed Boro defender Harry Coates of possession on the edge of the box, but again sent his effort wide when well placed.
The score remained at 1-0 to hosts Gateshead heading into the interval.
Gateshead continued to push for a second after the interval and came close twice, first via JJ O’Donnell’s close-range header and again as Paul Blackett fired straight at Tommy Taylor in the Boro goal.
Blackett had more joy in front of goal just after the hour-mark though, driving into the Boro box before finishing calmly into the bottom corner giving Taylor no chance.
John Deacey's Boro managed to pull a goal back on 73 minutes through substitute Flynn McNaughton, who slammed home following a cross into the penalty area.
O’Donnell's late penalty wrapped up the 3-1 win for the hosts before Boro's Jordan Deacey was dismissed following a scuffle.
Boro hit the road to take on Eccleshill United on Tuesday night.
Scarborough Athletic: Taylor; Lacey (Barkworth, 45’), Howarth (Johnson, 65’), Spence (Watson, 45’), Coates, Lowe, Dawson (Davidson, 54’), Deacey, Walshaw, Coulson, Brooksby (McNaughton, 65’). Unused subs: Morgan.