Hillsborough boss Brian Laws wants his side to finish with a flourish and they duly obliged with Whelan notching his 12th of the season.
Wednesday, chasing their third win in a row, carved out an early half-chance, Chris Brunt's deft corner evading the Ipswich defence as striker Leon Clarke connected at the far post pulling his header wide from six yards.
Ipswich, who have banged in ten goals in three games, including a 5-1 weekend thrashing of Wednesday's neighbours Barnsley, almost snatched the lead on 17 minutes after winning a free-kick on the edge of the area.
Striker Alan Lee, stroked in a curling right-foot shot, tipped over the top by Everton's on-loan keeper Iain Turner, who had not been on the losing side since arriving at Hillsborough five weeks ago.
Magilton's side, with Owen Garvan controlling the midfield, were caught out by the lively Brunt as he closed in on goal before delicately picking our Lee Bullen at the far post whose effort was pushed away by Lewis Price.
Wednesday went ahead in the 47th minute, Whelan bursting from midfield before beating the exposed Price with a low right-foot strike from just inside the area.
Centre-back Jason De Vos saw his close-range effort cleared as Wednesday broke quickly, Whelan crossing to MacLean whose downward header at the far post was blocked by the keeper's feet.
MacLean finally beat Price in the 59th minute as Kenny Lunt threaded the ball to the ex-Rangers striker who coolly swept the ball beyond the keeper's reach from 15 yards.
Gavin Williams hit the post with a free-kick seven minutes from time and substitute Dan Harding lashed the loose ball over the top before Turner kept out Garvan as Ipswich staged a late rally.