Hales hit 110 from 107 balls as England thrashed the hosts by 186 runs in Barbados to seal a 3-0 series win.
The 28-year-old did not tour Bangladesh because of security concerns and fractured his hand in India in January.
He said: "The last six months have been frustrating, so to score a hundred in my first game back is a great feeling."
Hales, who said it was his most important century for England, added: "Obviously when I chose not to go to Bangladesh, I knew I was opening up a spot for other people to come in and perform well.
"That was the risk I was taking, then the injury in India came at a really bad time for me. But I'm pleased the team have backed me and stuck with me. Hopefully I've repaid their faith."
Hales shared a 192-run partnership with fellow centurion Joe Root, who made 101, as England scored 328 from their 50 overs.
The game was virtually over once West Indies fell to 13-3 with only Jonathan Carter (46) offering serious resistance as the hosts were bowled out for 142 in 39.2 overs.
Man of the series Chris Woakes (3-16) and Liam Plunkett (3-27) did most of the damage with Steven Finn taking 2-35 while Ben Stokes and Adil Rashid picked up a wicket apiece.
England captain Eoin Morgan told Test Match Special: "Joe Root and Alex Hales really capitalised on their partnership, scoring the guts of our runs on what was a really tricky wicket to bat on. I thought they put us far past a par total - it was probably more of a 250 wicket.
"I'm a huge fan of time off and it was forced on Alex with a broken hand. Coming back as hungry and determined as that shows the huge competition for places in the side.
"Sam Billings didn't do a great deal wrong but unfortunately missed out today and Alex Hales comes back in at the top of the order and produces a match-winning performance, which is really outstanding.
"Picking 15 players is going to be hard for the Champions Trophy. Competition for places is really strong."
England have two ODIs against Ireland before opening their Champions Trophy campaign against Bangladesh at The Oval on 1 June.
England opener Alex Hales said it was "very emotional" to score a hundred against West Indies in only his third one-day international in six months.