The ICC also announced that Ravi Ashwin had been voted as its Cricketer of the Year for 2016.
Cook, who has led England to only one win in their last eight matches, was selected to head the ICC side picked by former Test greats Rahul Dravid, Gary Kirsten and Kumar Sangakkara for the sport's world governing body.
The trio based their decisions on player performances between September 14, 2015 and September 20, 2016, a period not covering England's 4-0 drubbing to India, Cook's fourth straight loss as captain.
Cook's England lost a three-Test series 2-0 to Pakistan in October 2015. Overall in the period he led England in 14 matches, with six wins, three draws and five losses.
He has been picked alongside Joe Root, wicketkeeper Jonny Bairstow and Ben Stokes.
Root has become the focal point of the batting order in recent years and averages 52.80 in his Test career while Yorkshire team-mate Bairstow broke a 16-year record for the most Test runs in a calendar year by a wicketkeeper in 2016.
Stokes's performances with bat and ball have helped him to establish himself as England's first-choice all-rounder.
There was no place in the XI for India skipper Virat Kohli, who sits second in the ICC Test batting rankings, while number one batsman in the world and Australia captain Steve Smith is the 12th man in the squad.
Opener David Warner, Adam Voges and Mitchell Starc are the three Australians chosen by the committee, with Kane Williamson picked from New Zealand.
Spinner Ravi Ashwin, who helped India to a 4-0 victory over England, is India's sole representative while Sri Lankan left-arm spinner Rangana Herath and seamer Dale Steyn of South Africa complete the line-up.
The ICC also announced that Ashwin had been voted as its Cricketer of the Year for 2016.