The 1872 Cup is awarded to the aggregate winners of the derby double header and the Warriors won the first contest 23-14 at Scotstoun following a fast start - before repeating the first-half onslaught in the capital.
Glasgow had nine fingers on the trophy and the RaboDirect PRO12 points almost sewn up after 40 minutes, taking a 16-3 lead courtesy of tries from New Zealand-born, Scottish-qualified wing Sean Maitland and Ruaridh Jackson, plus two penalties from Peter Horne, who was also sin-binned.
A Greig Laidlaw penalty was the solitary reply for Edinburgh, who last won the 1872 Cup in 2008-09, and their hopes were hit further when Allan Jacobsen was sin-binned and Henry Pyrgos scored a try.
Roddy Grant's converted score after 59 minutes gave the hosts some hope and Tim Visser scored five minutes from time, with Laidlaw kicking his side within four points.
But the late rally ended there as Glasgow saw out the remaining seconds to retain the derby bragging rights they have held since the 2009-10 season.
Watching interim Scotland head coach Scott Johnson will have been warmed by Glasgow's display with the RBS 6 Nations in mind, but, until the final 20 minutes, the Scotland players in Edinburgh's ranks did little to enhance their reputations with places at stake for the Calcutta Cup opener with England at Twickenham on February 2.
Only a win for the hosts by 10 points or more would prize the trophy from Glasgow, but that contest ended early on.
Glasgow's forwards bullied their Edinburgh counterparts in the first half and the hosts' game was riddled with errors.
The visitors won a penalty at the first scrum and forward momentum ensued.
Jackson received quickly recycled ball, drew his man and Maitland, on a good line, crashed over. Jackson missed the conversion.
Laidlaw kicked a penalty following a late aerial challenge by Stuart Hogg on Greig Tonks, before Horne was sin-binned for a tip-tackle on Matt Scott, who had not even received the ball.
That was as good as it got for Edinburgh in the first period as they failed to trouble short-handed Glasgow, with Laidlaw missing a simple kick to put his side a point ahead and Horne returning with the visitors' two-point lead intact.
Captain Laidlaw's attempt to spark Edinburgh with a quick-tap backfired as fly-half Piers Francis' pop-pass towards Netani Talei was intercepted by Jackson, who had enough pace to hold off Tonks and score in the left corner. Horne's conversion attempt hit the post.
Hooker Dougie Hall had a try curiously disallowed before Horne kicked two penalties to give the visitors a healthy half-time lead; their advantage in the 1872 Cup contest a near-unassailable 22 points.
Glasgow resumed on the attack and Van der Merwe was denied by the television match official after David Denton's tackle forced him into touch.
Sean Lamont, Jackson and Van der Merwe contrived to make a mess of another scoring opportunity as Glasgow threatened again before Jacobsen was sin-binned for playing the ball on the floor.
Pyrgos dropped over for Glasgow's third try immediately but Horne again missed the conversion before Edinburgh claimed a lifeline entering the final quarter.
Scott retrieved Laidlaw's chip and Grant powered to the line.
Laidlaw converted but the good work should have immediately been undone.
Van der Merwe bounced through five tackles and presented the ball to Hogg, who dropped it over the try-line.
Glasgow were ruing the mistake, which also saw them miss out on a four-try bonus point, five minutes from time as Visser came in field to score from replacement Richie Rees' pass.
The visitors, though, survived the remaining time to triumph.