The Team BMW driver from Portadown finished second in the wet race three, coming home behind Honda's Shedden.
Turkington was later awarded the victory, the first for Team BMW, ahead of Adam Morgan and Ash Sutton.
Aiden Moffat, who collected his maiden win, and Tom Ingram were the other race winners in an eventful day.
Turkington had a strong start to the weekend, working his way up to fourth after starting in 10th place.
Yellow flags at the final chicane meant he couldn't pass Rob Austin despite being the quicker driver in the latter stages of the race.
In race two, Turkington struggled on the soft tyre in the opening stages of the race before going on a charge at the end, overtaking reigning champion Shedden with two laps to go to claim fifth.
Turkington completed a solid weekend in race three, coming home behind Shedden after overtaking pole sitter Dave Newsham on lap nine.
The race was initially red flagged after several cars aquaplaned off the circuit, and the race was reset after a brief wait for the conditions to clear up.
Turkington leaves Donington Park second in the standings, 15 points behind Ingram.
It was another luckless weekend for Carrickfergus driver Chris Smiley, whose strong pace didn't yield the results it deserved.
Starting 20th, Smiley worked his way up to 16th before being punted off by Tom Chilton, taking both drivers out of the race.
After his first race incident, Smiley started race two from 26th, dropping down to 29th by mid-race.
A sensational final five laps moved the 25-year-old up the order, crossing the line in 17th place and his best result of the season.
Smiley made the most of the torrid weather conditions in race three, moving his way up to seventh place before the red flag reset the order.
The BTC Norlin driver was forced to start from the pit lane at the restart, coming in 18th but moved up to 17th following Shedden's disqualification.
In the support races, Northern Ireland racers had a successful weekend at the East Midlands circuit.
Belfast's Charlie Eastwood dominated in the Porsche Carrera Cup, taking pole position for both races as well as collecting both wins as he continued his strong start to the championship.
Eastwood has now taken the lead in the championship, four points ahead of team-mate Daniel Cammish.
Hillsborough teenager Dan Harper had a strong weekend in the Ginetta Junior series, taking victory in the second race.
Another podium and a sixth-placed finish means that Harper leaves Donington second in the championship table, five points behind Tom Gamble.
At the first round of the European Le Mans Series at Silverstone, Templepatrick driver Wayne Boyd claimed a podium for United Autosports.
Colin Turkington was moved up from second to first place at Donington Park after Gordon Shedden was disqualified for failing a ride height test.