The president now has 53.1 million followers, according to his account page.
"These sudden changes in account behavior could include Tweeting a large volume of unsolicited replies or mentions, Tweeting misleading links, or if a large number of accounts block the account after mentioning them", it further explained.
Katy Perry, the most followed person on Twitter, lost over 2.8 million followers in total, falling from just over 109 million earlier this week, to little more than 106 million on Friday.
The move is aimed at users reportedly inflating their followers on the platform with automated or fake accounts, buying the appearance of social influence to "bolster their political activism, business endeavours or entertainment careers".
Uhuru, who is the most followed Kenyan on Twitter, had 3,234,935 followers as of July 12 but lost 16,071 of them in the purge.
Twitter has been under increased public scrutiny over complaints of fake and automated Twitter profiles that are spreading fake news, spamming the micro-blogging site, abusing others or impersonating people.
It added, "This week, we'll be removing these locked accounts from follower counts across profiles globally".
By cracking down on fake accounts, Twitter hopes to restore faith in the controversy-ridden platform where influence-from entertainment to politics-can be inflated by automated or fake followers, the New York Times reports.
While BJP President Amit Shah was left poorer by 33,363 followers, Delhi chief minister Arvind Kejriwal has lost 91,555 followers.
Although losing 2 million followers is undoubtedly a significant drop, proportionally speaking it's not necessarily huge.
On Wednesday, Twitter said it was making the change in order to boost the credibility of follower-count numbers and improve transparency.
Prominent people and celebrities have started noticing the drop in followership. Shah Rukh Khan lost nearly 3.5 lakh followers (35.7 million) while Amitabh Bachchan registered an even bigger loss, at over 4 lakh (34.5 million).