Pompey suffered late heartbreak at Rotherham where the hosts' winner left Kenny Jackett's team with a haul of just one point from three games in 2018.
They drop to ninth, now four points off the top six, after Joe Mattock's 91st minute header condemned them to defeat at the New York Stadium.
With Sylvain Deslandes given his debut in defence and Matt Kennedy back in the starting line-up, Pompey gave as good as they got in the first half with Jamal Lowe, Kennedy, Brett Pitman and Dion Donohue all threatening the home goal.
Luke McGee had to be on his toes a couple of times at the other end.
The second half, as Jackett admitted afterwards, largely saw the Millers in charge.
Pompey's inability to boss the game saw Oli Hawkins and Connor Ronan brought on midway through the half but they could do little to affect the balance of things.
It looked like the Blues would hold on for a point only for two ex-Pompey players to combine to break their hearts as Michael Smith crossed for Mattock to head in.
Jackett told the Pompey website: 'There have been a few late goals that have cost us now and that’s obviously disappointing. I thought that we’d ridden the storm in the second half and the game appeared to just be petering out.'
The Blues aim to recover when they host third-placed Shrewsbury next Saturday.
Pompey: McGee; Thompson, Burgess, Clarke, Deslandes (Ronan 66); Close, Donohue; Lowe, Naismith, Kennedy; Pitman (Hawkins 66). Subs not used: Bass, Widdrington, May, Bennett, Chaplin
Referee: Robert Jones
Attendance: 9,129 (1,471 Pompey fans)
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