The Lionesses took the lead through Lucy Bronze and Lauren Hemp doubled the lead at Sunderland's Stadium of Light.
Scotland got one back just before the break through Kirsty Hanson but were unable to find a second half equaliser.
England have three points in the four-team Nations League group along with Belgium, who beat the Netherlands.
Just over a month after their painful World Cup final defeat to Spain, England were on the front foot straight from the kick-off.
Lauren James threaded a pass to Rachel Daly, whose low effort was saved by Lee Gibson.
England thought they had broken the deadlock in the 25th minute through Daly's flicked header from a corner, but the celebrations were quickly cut short when the goal was ruled out for offside against Chloe Kelly in the build-up.
Bronze opened the scoring after a cross from Katie Zelem picked out the right-back, who made a perfectly timed run to head home.
They doubled the lead in the 45th minute as Daly picked out Hemp and the Manchester City winger headed into the top corner.
Scotland reduced the deficit with the last kick of the half as England failed to clear their lines and Hanson prodded into the bottom corner.
Scotland had a chance to level when England keeper Mary Earps punched Rachel McLauchlan's cross to Hanson, who smashed her shot off the crossbar.
The visitors threatened again with six minutes to go, with Lisa Evans picking out Christy Grimshaw on the edge of the box but her low effort was held by Earps.
