Test captain Root recently decided to sit out the Twenty20 Tri-Series against Australia and New Zealand, giving himself the chance to appear in the IPL.
He said the financial side of the tournament was an appealing factor, together with the prospect of improving his white-ball skills.
But Root, man of the series as England beat Australia 4-1 in their run of one-day internationals this month, was not bought this weekend.
He was joined on the unsold list by county colleagues Jonny Bairstow, Liam Plunkett, Adil Rashid and David Willey.
Fast bowler Mark Wood landed a deal with Chennai Super Kings and was taken aback that several of his England colleagues were not signed up.
Asked about Root not landing a deal, Wood said: “I am surprised, and not just him... Morgan, Halesy, Pudsey (Liam Plunkett) who took the most wickets last year. Joe is world class in any form so I am surprised and incredibly lucky I’ve been picked up.”
Bidders may have been put off Root because he would need to be back in England before the end of the tournament to prepare for a Test series against Pakistan.
After Root went unsold on Saturday, it was the turn on Sunday of one-day skipper Morgan to be snubbed despite previous experience with Royal Challengers Bangalore, Kolkata Knight Riders, Sunrisers Hyderabad and Kings XI Punjab.
Opener Hales was also not signed up despite sitting eighth in the Twenty20 international batting rankings.
Fast bowler Tymal Mills, the second most expensive buy in 2017, and left-arm seamer David Willey were among the other England players to miss out.
Fellow quick Wood, back in the England limited-overs side after his latest injury absence, was sold for £167,000, while wicketkeeper-batsman Sam Billings - recently appointed Kent captain - will join him at Chennai after he went for £71,000.
Wood said: “I was pretty relaxed ... if it doesn’t happen, it doesn’t happen, but I’m delighted to be picked up and go to a fantastic world tournament and get the chance to play with some of the best players and learn new things.
“Playing under (Chennai captain) MS Dhoni will be fantastic, that’s something anyone would dream of and love to do. Dwayne Bravo is another one, he’s got an unbelievable slower ball so hopefully I can try and pick his brains and pick one up too. It’s a good place to go and hopefully come back to England with some new tricks.”
Paceman Chris Jordan, who like Billings has played in the IPL before, was bought by Sunrisers Hyderabad for £110,000.
Ben Stokes was sold for almost £1.4m on Saturday despite his impending court appearance.
The England all-rounder was snapped up by Rajasthan Royals, although the figure does represent a decrease on the £1.7million Rising Pune Supergiant paid last year.
Stokes, 26, who was named the IPL’s most valuable player last year, was again listed as one of 16 marquee players. He is due to appear at Bristol Magistrates’ Court on February 13 charged with affray.
With the IPL having assured franchises before the auction they would be able to replace Stokes if he was ruled out for the whole competition, the Durham player fetched the highest price.