Southampton loanee Josh Sims, a second-half substitute, teased the home team down their left in the 79th minute, before laying the ball off for Reece James to turn and curl into the net from 14 yards out.
It was a rare piece of quality in a game which would have done little to persuade absent League One fans they were missing out.
“I’m delighted to get our first clean sheet of the season and to come to a tough place and get it makes it even sweeter,” defender Joe Wright said.
“We had to dig deep today but I thought we stuck to our game plan and we did really well.
“It was a good team performance.
“Second half we had to dig deep a little bit but first half, I thought we controlled the game.”
Doncaster had the better of an uninspiring first half and created the best of the half-chances, as it took Pompey around 35 minutes to enjoy a decent spell of possession.
Yet the closest either team came to breaking the deadlock was when home defender Sean Raggett sliced a defensive clearance wide when cutting out a dangerous James cross.
Ten minutes after the break, Fejiri Okenabirhie forced Pompey keeper Craig MacGillivray into a full-length save but that was as exciting as it got until James scored the winner.
Doncaster are seventh after five games, on 10 points.
Portsmouth: MacGillivray, Johnson, Whatmough, Raggett, Brown, Naylor, Close (Williams 81), Harness, Cannon, Curtis (Jacobs 59), Harrison (Marquis 63). Unused substitutes: Nicolaisen, Morris, Pring, Bass.
Doncaster: Bursik, Halliday, Wright, Anderson, John, Gomes, Whiteman, Taylor (Sims 63), Coppinger (Richards 64), James, Okenabirhie (Smith 90). Unused substitutes: Lokilo, Jones, Williams, Butler.
Referee: B Huxtable (Devon).
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