A gripping contest looked sure to go right to wire when it was poised at 6-6, but Selby proved the stronger player in the closing stages as he reeled off four in a row to end Murphy's challenge.
Selby was guaranteed to regain the world number one ranking regardless of today's result, but it would have meant little to him if he had gone back to Leicester without the trophy. He had won just two of his previous seven ranking finals so was determined to show that it's titles as well as consistency that has brought him to the top of the sport.
A prolific break-builder who scored a record 55 century breaks last season, Selby was not at his free-flowing best in today's final, and indeed Murphy looked the better player for much of the contest. But 29-year-old Selby's tremendous capacity to cling to his opponent through tactical nous and potting vital balls allowed him to stay in touch, and eventually move up a gear. He goes home with a cheque for £125,000.
Though he has thrived in the Players Tour Championship series this season, Selby has struggled in the main ranking events, and there were doubts as to whether the neck injury he suffered at the end of last season was still troubling him. But he has put those doubts to rest by winning one of snooker's two most prestigious ranking events for the first time. He adds the UK crown to the Masters titles he won in 2008 and 2010, and his sights must now be set on the World Championship. Judd Trump held the number one ranking for just five weeks and Selby now has a healthy lead at the top of the list.
Sale-based 30-year-old Murphy, who couldn't reproduce the blistering sequence of scoring which saw him come from 8-4 down to win his semi-final against Ali Carter 9-8, missed out on the chance to become only the eighth player to win the UK title more than once, having beaten Marco Fu in the 2008 final. He remains at number four in the world and is £50,000 richer for his efforts this week.
Selby won the last two frames of the afternoon session to make it 4-4 and looked set to make it three in a row in the first of the evening session when he made a break of 58. But he then missed two simple reds to a centre pocket and Murphy punished him with a cracking 65 clearance.
Murphy also had a chance to clear from 43-8 behind in frame ten, but ran out of position on the final yellow. He then failed to leave the yellow safe when escaping from a snooker, and Selby was able to add the points he needed for 5-5.
In the 11th, Selby missed the last red to a centre pocket, and Murphy cleared to the pink but then went for a very difficult long pot along a side cushion, and rattled it in the jaws leaving Selby to tap it home to take the lead. Murphy compiled runs of 39 and 38 to make it 6-6 at the mid-session interval.
The 13th saw Selby make 51 before missing a frame-ball red. Murphy took it to the colours but lost a safety battle on the yellow and his opponent regained the lead. And Selby then took a two-frame advantage for the first time in the match with a cool 98.
In the crucial 15th frame, Murphy had a chance to win it from 50-1 behind, but he missed the blue off its spot after potting the last red. A grateful Selby took advantage to go 9-6 ahead, and breaks of 25 and 38 helped him through the 16th to secure victory.
Selby said: "It's a really proud and special moment. I'm a bit disappointed with the performance but a win's a win. Over the whole tournament I've only played well in frames rather than matches, and I've only really played well in patches, and here I am sat as the UK champion. It's strange.
"I think there were four or five frames today where I got 40 or 50 points in front and then Shaun would give me golden chances to win the frame and I didn't finish them. I missed a lot of easy balls. I put a lot of pressure on myself going out there today because it's not every day you get to a UK final.
"Hopefully the neck injury won't come back, if it does I'll have to cross that bridge when it comes. I did have some doubts after the injury, but I always felt that I could get back and play well in tournaments again. At the same time, the confidence was gone and I'm still getting that back now. I love the game and when you're sat at home watching other people winning tournaments it is quite upsetting."
A gracious Murphy added: "Fair play to Mark - he played some very good shots and that's why he's the champion. Going into tonight it was best of 11, which is what we've been playing all week. I felt very positive and when I stole the first frame I really fancied the job, but in the last session he went up a couple of gears and I didn't keep up.
"In any sport you can only take so much punishment, but it's the frames you know you should win that really hurt and there were plenty of those for me tonight.
"I'm very pleased for Mark, he's one of my best mates, I feel some of the criticism he's had over the last year has been unfair and unfounded, and been said by people who don't know what they're talking about. He can only try his best. This victory will be all the sweeter for him because of all he's been through.
"I came here with a new idea, going back to my old attacking style, and it got me the runners-up spot, so I'm going to go back and do some more practise, because I've got a PTC event in Scotland next week."
Ball by ball scoring and results from tournaments