Vydra, who was also in contention for the young player honour, has scored 20 goals in the Championship for Watford following his loan move from Udinese.
The Hornets are keen to keep the Czech Republic forward on a permanent basis, but Vydra has attracted interest from the Premier League.
He beat Crystal Palace striker Glenn Murray, who has scored 29 goals in 34 Championship appearances this season, and Ince to the award.
There was consolation for Ince in the young player category as he was rewarded for scoring 18 goals for Blackpool this season.
Ince was heavily linked with a January move to his former club Liverpool, along with Capital One Cup winners Swansea City, following his exploits at Bloomfield Road.
In addition to beating off Vydra to the prize, Ince also edged out last year's winner - Crystal Palace winger Wilfried Zaha - was on the short list.
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.