The Sky Blues have failed to beat the Tractor Boys home or away in any competition since October 1994.
Ipswich strikers Jon Macken and Alan Lee were the difference with two second-half strike separating the sides, with Michael Doyle replying late on for the Sky Blues.
It saw Coventry slip to their third successive defeat, proving a miserable Christmas for manager Micky Adams.
Coventry received a blow before the game started when inspirational skipper Rob Page pulled out of the side with his wife in labour, having their third child.
But the Sky Blues started the brighter of the two sides and Leon McKenzie's mazy run in the second minute found his way to the by-line as he beat Alex Bruce.
McKenzie's cross eventually found its way to Colin Cameron, but the 34-year-old's shot on the half volley flashed wide.
Ipswich immediately responded and should have taken the lead in the fourth minute. Macken played a one-two with Lee in Coventry's penalty box and the former Manchester City striker put his shot wide when he really should have done better.
Ipswich started to dominate in midfield and a ball into the box got Lee away, who fell under the challenge of Elliott Ward. The Suffolk side appealed for a penalty, but Northumberland referee Clive Oliver booked the forward for diving.
Coventry almost took the lead just before half-time as a long ball from Clive Clarke found McKenzie, who saw Ipswich keeper Lewis Price off his line but his lob from 35 yards fell just wide.
The second half started as tightly as the first half had been with both sides struggling to gain midfield dominance.
A shot from Ipswich's teenage midfielder Owen Garvan from the edge of the penalty area deflected off of Coventry's Richard Duffy and keeper Andy Marshall did well to push the ball behind.
But Ipswich took the lead in the 61st minute following a corner from Gavin Williams.
His cross was met by Richard Naylor's header which Marshall pushed onto the post, but on-loan Crystal Palace forward Macken made amends for his earlier miss by scoring.
Coventry responded by making three quick substitutions bring on Kevin Kyle, Chris Birchall and Marcus Hall.
It almost paid off as Kyle found McKenzie, but his flighted shot was brilliantly tipped over by Price.
Coventry again went close as Birchall's cross found Kyle, but his shot from point blank was smothered by Price.
But the game was over as Lee got his head to a Billy Clarke cross in the 85th to put the result beyond doubt, leading to a chorus of boos from the home side.
Doyle scored an 89th minute consolation for Coventry from the edge of the area after a poor clearance from defence, but it proved too little too late.