James Norwood pulled a 37th minute goal back for Town after Tyler Smith and Tom Nichols had scored for Bristol Rovers with the scoreline 2-1 to the visitors at half-time.
Town boss Paul Lambert made six changes from the side which exited the FA Cup to Coventry on Tuesday.
Tomas Holy kept his place in goal with Cole Skuse skippering with Luke Chambers still out with his neck injury.
The veteran Bristolian, who was with Rovers as a schoolboy, made a rare start at right-back with Janoi Donacien unwell. Luke Garbutt was on the left with James Wilson partnering Luke Woolfenden at the centre of the defence.
Lambert returned to the midfield three which impressed in the first half of the 1-1 league draw at Coventry last Saturday, Andre Dozzell, Flynn Downes and Jon Nolan.
Up front, Will Keane started down the middle with Kayden Jackson on the right and James Norwood on the left.
Teddy Bishop and Freddie Sears were among those who warmed up on the pitch beforehand as they continue their recoveries from injury but weren’t included in the 18.
The Pirates, wearing yellow and black, were without 10-goal star striker Jonson Clarke-Harris and full-back Mark Little along with suspended midfielder Abu Ogogo. Former Blue Ed Upson started in the midfield.
Town won a corner in the opening minute which was cleared to Nolan, who volleyed over from not too far outside the box.
However, the visitors took the lead with their first attack of the game only four minutes later.
A quickly-taken Luke Leahy long throw on the left came across the box, Ollie Clarke held off his man and Tyler Smith used the space created to beat Holy from just inside the area.
The Pirates, who last won at Portman Road on Boxing Day 1958, should have been two in front only three minutes later when Rollin Menayese was allowed a free header from a Liam Sercombe corner on the left but nodded over when it appeared easier to hit the target.
On 10 Sercombe shot not too far over from distance with the Pirates having all of the early chances.
The Blues had had one or two decent spells on the ball but without creating a chance and while looking distinctly shaky at the other end.
In the 13th minute Nolan played a clever ball through for Jackson, the former Accrington man took it past advancing keeper Anssi Jaakkola but very wide and the danger was snuffed out.
The Blues briefly started to get on top, winning a series of freekicks - with Upson shown the first yellow card of the game for a foul on Nolan - and corners on the left in the minutes that followed. On 16 Norwood might have equalised as the ball came in from the left following a flag-kick but failed to get a touch.
However, the Blues continued to look unsure of themselves at the back and misplaced passes and miscommunication began to become commonplace.
And on 25 Rovers went two in front. Alex Rodman was found on space on the right and sent over a cross which Tom Nichols stooped to nod home at the far post.
The home crowd made their frustrations at a second Pirates goal and a disappointing Blues performance evident as the visitors celebrated.
Town were close to pulling a goal back on the half hour when Jackson was sent away on the right and sent over a dangerous low cross. Keane failed to get a decent contact on it and Nolan behind him could only slam against keeper Jaakkola as he closed the space.
The Blues were by now dominating possession and were regularly winning corners with the pressure beginning to grow.
On 36, after excellent work from Woolfenden on the left following another flag-kick, Jackson saw and effort saved by Jaakkola, then Garbutt’s powerful strike was blocked.
But Town kept the Pirates pinned back in their half and a minute later the Blues reduced the visitors’ advantage.
A slick move Woolfenden flicked on to Nolan, who turned on to Jackson, by now on the left, who took the ball on before sending over a cross to the far post which Norwood breaking in from the right nodded into the net.
Having pulled a goal back the Blues went looking for another. Referee James Adcock turned down and appeal for penalty after a Norwood shot hit Alfie Kilgour on the hand, then moments later the former Tranmere man guided a Garbutt cross from the left straight into the keeper’s arms.
The Pirates were the next to threaten, Leahy sending in a 43rd minute cross for Smith whose header was well-saved low down to his left by Holy.
As the game moved into two minutes of injury time, Rovers skipper Ollie Clarke needlessly reacted to a Downes challenge on Upson, leading to a brief outbreak of handbags. Order was quickly restored and referee Adcock booked Clarke and Downes.
Town continued pressing in the final minute or so with Norwood and Nolan both having strikes blocked, before Menayese somehow diverted the ball wide of his own goal at the near post ahead of Norwood as a low cross came in from the right.
The whistle ended a rollercoaster half soon afterwards with the Blues having done enough to get themselves back on terms.
After a poor start and some very shaky defending as the makeshift backline struggled their feet and conceded the two Rovers goals, Town dominated and might have pulled one back prior to Norwood’s eighth of the season.
From there, the Blues - who had had 68 per cent of the possession - had further opportunities to score. If they continue the second half as the finished the first then Rovers will do well to maintain their lead.
Town: Holy, Skuse, Wilson, Woolfenden, Garbutt, Nolan, Downes, Dozzell, Jackson, Norwood, Keane. Subs: Norris, Judge, Nsiala, Kenlock, Dobra, Georgiou, Huws.
Bristol Rovers: Jaakkola, Craig, Upson, Sercombe, Clarke, Nichols, Leahy, Kilgour, Smith, Menayese, Rodman. Subs: Van Stappershoef, Kelly, Tomlinson, Adeboyejo, Hoole, Hargreaves, Phillips. Referee: James Adcock (Nottinghamshire).