Pompey's Noe Pamarot appeared to get the final touch when Windass headed a corner by fellow substitute Stelios Giannakopoulos but Hull No2 Brian Horton said: "Try taking it off Deano.
"When the ball came in he had to get some pace on it and to my mind he did that and he's certainly claiming it."
Windass, who scored the winning goal in last season's promotion play-off final against Bristol City at Wembley, was making only his third substitute appearance of the season for the Tigers.
Teddy Sheringham was 40 years and eight months when he scored for West Ham in a 2-1 defeat by Pompey at Upton Park on Boxing Day 2006 but Portsmouth manager Tony Adams insisted: "It was an own-goal today as far as we're concerned - down to Noe I'm afraid.
"But we had enough chances to win this one, although I always thought we needed a two-goal cushion to make sure."