Vydra, one of Watford's loan stars from Italian side Udinese, beat off competition from Ince and Crystal Palace forward Glenn Murray at a ceremony in London.
Vydra has scored 20 goals this season to spearhead the Hornets' bid for promotion under Gianfranco Zola.
Murray missed out on the award despite notching 29 goals so far this term, a return which put him second only to Lionel Messi in Europe's top leagues.
Ince was able to celebrate, however, after being named the Johnstone's Paint Young Player of the Year.
The 21-year-old, now managed by his father Paul, has hit 18 goals despite Blackpool's struggles this season.
Ince pipped Vydra and last year's winner, Crystal Palace's Manchester United-bound winger Wilfried Zaha.
He said: "It's been a whirlwind 18 months for me. It's been fantastic. I left Liverpool to get games in the Championship and I'm enjoying it at Blackpool.
"It's a proud moment for me and my family."
Nottingham Forest striker Simon Cox's goal against Birmingham City back in September was voted the Goal of the Year.
Cox produced a deft touch to bring Lewis McGugan's floated pass under control before producing a superb finish to lift a volley over keeper Jack Butland.
It was a double win for Forest as goalkeeper Dimitar Evtimov, who is yet to make his first-team debut, took home the Apprentice of the Year award for the Championship.
The Bulgarian saw off competition from Duane Holmes of Huddersfield Town and Watford's Bernard Mensah to claim the prize.
The prize for the Family Club of the Year went the way of a Championship club as current leaders Cardiff City were rewarded with the honour, while Charlton Athletic were named the Community Club of the Year.
Brighton & Hove Albion full-back Inigo Calderon was named the PFA Player in the Community, while Billy Neil of Millwall was the Unsung Hero award winner.
The League One award went to Matt Ritchie, who started the season with Swindon before moving to their promotion rivals Bournemouth in January, with Port Vale's 25-goal striker Tom Pope collecting the League Two gong.
Bradford boss Phil Parkinson was rewarded for his unfancied side's remarkable run to the Capital One Cup final with the Outstanding Managerial Achievement award.
He said: "I'm very honoured to receive this award. My name might be on it but it is a team award. Not just the team on the pitch but the team off it as well."
And legendary former England goalkeeper Peter Shilton, who played more than 1,000 Football League matches, accepted the Contribution to League Football award.