The Heed have confirmed the permanent appointment following his time in interim charge at the International Stadium last season.
Elliot, who will work alongside Louis Storey, impressed after taking over following Mike Williamson’s move to Milton Keynes.
The club finished sixth but were ultimately denied the chance to compete in the play-offs, putting their agony to one side to go on and lift the FA Trophy.
The progress made was enough to convince the club’s board that they need look no further for a full-time manager.
Chairman Neil Pinkerton said: “We’re delighted to finally banish the interim tag for Rob and Louis.
“It was always our intention to sit down at the end of the season and agree terms, which we have now successfully concluded.
“Rob, Louis and the entire team have been relentless in the off-season, so rest assured that we’re well-placed in terms of our on and off field recruitment plans.”