Pompey's failure to score at home extended to a sixth Barclays Premier League game.
Fabio Rochemback's absence with a knock picked up at Birmingham completed a daunting casualty list for beleaguered Boro boss Gareth Southgate who has seldom been able to pick his preferred front-line combination of Aliadiere and Mido, with the former Tottenham player still out with a groin injury.
Boro's Turkish striker Tuncay was the first to show some purpose in a scruffy start, shooting on the turn wide of David James's left-hand post, with the keeper confidently looking on.
Utaka's mazy run on the right finally brought him into the Boro area and although he was challenged as he attempted to shoot the ball ran loose for Niko Kranjcar on the edge of the box to fire a low drive which Mark Schwarzer smartly held.
Sol Campbell had to time his tackle just right to deny Tuncay when Boro broke back and from the resulting corner Kanu was back defending.
Neither side showed much creativity in the opening 20 minutes, Kranjcar having a goalbound free-kick blocked by an efficient Boro wall after Shawky manhandled Kanu off the ball and Stewart Downing's set-piece also blocked at the other end following a clumsy foul by Papa Bouba Diop on Tuncay.
But then Boro gratefully collected a soft goal and a surprise lead as Pompey dithered at the back.
Downing's cross from the right sailed beyond the far post where O'Neil volleyed what looked like shot of little power. James fumbled and Tuncay, looking suspiciously offside, followed up to knock into an empty net for his fourth goal in six games.
Boro could have had a second but for Hermann Hreidarsson's quick thinking in the 25th minute. Another Downing cross, from the left this time, was glanced on by Tuncay and Lee looked a certain scorer until the big Icelander blocked his shot.
Kranjcar's quickly-taken free-kick produced a powerful 25-yard drive by Diop two minutes later as Pompey looked for an equaliser but the giant midfielder's effort was just wide.
Diop's massive figure seemed to be everywhere as he tried to urge Pompey on to greater efforts but Benjani and Kanu were getting little change out of Robert Huth and Jonathan Woodgate in the Boro defence.
When Utaka brought down Lee in the 35th minute, O'Neil was only a few inches away from scoring against his old team, curling a 20-yard free-kick just over the bar with James at full stretch.
When Pompey won a free-kick, though, it was O'Neil who was booked for encroaching as Utaka tried to touch the ball aside to Kranjcar. Referee Alan Wiley brought the kick ten yards forward to be re-taken but Utaka's second attempt was a poor effort straight into the wall.
Hreidarsson pushed forward to fire a shot that took a deflection into the side-netting for a corner but Diop could not force it home with his attempted header as Boro defenders surrounded him.
In first-half injury-time Benjani's cutback presented Diop with a wonderful chance to level matters but he stabbed a hurried effort over the bar.
HT: Portsmouth 0 Middlesbrough 1
Pompey replaced Hreidarsson with Matt Taylor for the second alf although it was not clear whether the Icelandic star was injured.
The game continued at a frenetic pace with sliding tackles all over the place but there was little cohesion until Lee slipped through on the right and drilled just wide for Boro.
Tuncay had tried to lob James after a long ball down the middle but the goalkeeper did enough to put him off.
Benjani was trying to wiggle his way through when Huth's meaty challenge bowled him over but referee Wiley waved away half-hearted penalty appeals - mostly from the crowd.
Redknapp tried another substitution, and striker David Nugent came on for Utaka after 63 minutes.
And, after the newcomer won a free-kick on the right, Pompey looked certain to equalise when Taylor crossed and Hughes knocked it back from the far post only for Kanu to drill against the woodwork from a few yards before Schwarzer gratefully cleared.
Boro defended their hard-earned advantage with admirable zeal but their determination brought bookings for O'Neil, Julio Arca, Luke Young and Woodgate in a frantic finish.
They pulled 10 men back behind the ball to resist Pompey's inevitable late rush and Woodgate and Huth performed a series of last-ditch tackles to keep the home side at bay.
Matt Taylor went into the book, too, for a desperate tackle on Boro substitute Adam Johnson.
FT Portsmouth 0 Middlesbrough 1