An even longer goal drought had been ended in the first minute of the game when Daryl Murphy marked his Ipswich debut with a goal after just 23 seconds.
Roy Keane raided his former club Sunderland to sign Murphy and David Healy on transfer deadline day and it paid dividends immediately.
Healy crossed from the right side and Murphy sent a shot into the bottom corner from 12 yards. It was the first time he had been on the scoresheet since scoring for the Black Cats in a 2-0 Premier League win over Wigan on February 9, 2008.
Healy and Murphy were two of four changes made by Keane. Elsewhere, defender David Wright and midfielder Jonathan Walters were restored to the starting line-up.
Boro boss Gordon Strachan also made four changes. Lee Miller and Kyle Naughton went straight into the side while fellow transfer-window arrival Stephen McManus made his debut and Andrew Taylor was recalled.
The sale of 12-goal winger Adam Johnson to Manchester City coupled with several players absent through injury and suspension saw Strachan start the game with three centre-halves and three full-backs.
It was immediately evident that players were playing out of position by the start they made to the game.
But Boro regrouped after conceding the early goal, although they posed little in the way of an attacking threat in the first half.
Chris Killen got an acrobatic effort on target on the half-hour mark but it was a routine save for Arran Lee-Barrett.
Healy and Murphy continued to look lively and had several shots blocked by Boro defenders before the visitors came into the game after the break.
Miller fired over the crossbar five minutes into the second half and Killen forced a fine save from Lee-Barrett when his shot inside the area was tipped around a post.
Boro's pressure paid off after 62 minutes when Wheater headed home Gary O'Neil's left-wing cross.
Ipswich had a chance to retake the lead with 12 minutes remaining when Gareth McAuley headed Grant Leadbitter's corner over the crossbar.