The Englishman holed a 54-foot putt for eagle on the 18th to set the clubhouse target at 20 under par after a scintillating closing 63.
Samooja, who was playing in the last group of the day, joined him to take the tournament to extra holes but a three-putt on the first trip back up the 18th handed Shinkwin his first professional victory.
“I’ve always wanted to win on the European Tour and now I have,” said Shinkwin, who collects 335 Race to Dubai points to climb up to 51st from 130th in the Rankings.
“The thing about holing that putt on 18th is that there is no chance normally of sinking that. It’s one in a million that you hole from that distance. My aim was to try and two putt and I holed it.
“It’s been a bit of a shock but it feels great. Commiserations to Kalle, he’s obviously played well this week as well, and I’m sure there are bigger things yet to come for him.”
Samooja, who was also searching for a first European Tour title, picked up 222 Race to Dubai points for his runner-up finish which sees him jump up 30 places to 36th and seal his spot in the DP World Tour Championship, Dubai.
Meanwhile, Jamie Donaldson, Garrick Higgo and Robert MacIntyre all collected 103 Race to Dubai points after finishing two shots back in a share of third. Higgo and MacIntyre both edge closer to sealing their spots in the DP World Tour Championship after moving up to 62nd and 57th respectively, while Donaldson climbs up to 104th in the Rankings.
This year’s US$8 million DP World Tour Championship is only five weeks away with some of the world’s best players set to take on the Earth course at Jumeirah Golf Estates from December 10-13. European Tour