Speaking from his holiday, the gaffer said of the man who made 34 appearances for the Town while on loan from the Championship club last season: "We are delighted to secure Shins for another two years.
"It was something we always had in mind and tried to do it permanent last year, but it wasn't a possibility so we took him on loan, and providing everything fitted into place, we wanted to do it for this summer.
"He had a frustrating time towards the end of the season, but that's not to diminish from the impact he had on the football club because in all the games that we played fantastically well, Andrew Shinnie was key.
"We think he can have an even bigger impact in League One and beyond, so we are really excited to have him under contract. He will have had other options, so it shows that he's bought into everything that we've done and he sees where we're going. He's an excellent signing for us."
The 28-year-old former Rangers and Inverness Caledonian Thistle man did not figure in Jones' matchday squads after the Good Friday defeat at Colchester – the game in which Luke Berry suffered a season-ending injury – but Jones insists he had already done his bit to help set promotion up.
"It's difficult sometimes and I keep saying to one or two of them that came out of the side towards the end of the season, including people like Shins and Luke, that they had a massive, massive impact," said Jones.
"They might have missed the last six, seven, eight games, or whatever it was, but the influence they had over the season was immense and we were the side that we were because of all our squad. Everyone.
"The way we train and the environment we have enables us to be a better side on a Saturday. They all contributed to that, and Andrew was a massive part of that both on and off the pitch, but especially on it for three-quarters of the season.
"We had no passengers. What we've had is a wonderful group and Andrew is a real part of that. He showed his importance to the squad and even though he was having a tough time himself, he still trained at the same levels, enhanced everything that we did on the training pitch, and kept his way about him around the place.
"That just shows he's a top class pro. If we'd flipped the season around and he'd had a slow start and finished the way he started, then he probably would have been slightly happier.
"But we might not have been the same side, or be in the same position we were at the end if he didn't have the impact he'd already had."
Confirmation that Shinnie is staying, after Alan McCormack recently penned a new one-year contract, bolsters a midfield stable that has been depleted in number this summer with Olly Lee joining Hearts after Jordan Cook and Lawson D'Ath were released.
"In theory we've lost three, with Jordan, Lawson and Olly going, so we don't add Shins because he was in our building anyway, but we have to make sure that we replace one or two of the three that have gone to make us competitive," added Jones.
"We've got good midfielders in the building in terms of Pelly-Ruddock and Luke Gambin, who we always saw for long-term, so that gives them a real opportunity – coupled with the fact that Elliot Lee has shown his versatility at being able to drop in.
"We have high hopes for Andrew and you may see him a different area, you may see him in a different position, but he'll be a key player for us and that's why we have invested everything we have in him."