On-loan Doncaster Rovers striker Iain Hume consigned managerless Portsmouth to a sixth straight defeat.
The Canada international took advantage of hesitation between Pompey goalkeeper Mikkel Andersen and skipper Brian Howard to slide the ball home.
Lee Williamson should have equalised for the home side after the hour mark but miscued his effort.
Pompey were frustrated late on when Izale McLeod lobbed over and a Gabor Gyepes header cleared the crossbar.
VIEW FROM THE DRESSING ROOM
Portsmouth caretaker boss Guy Whittingham told BBC Radio Solent:
"I was pleased overall with the effort of everybody. I think people can see that the effort was in there.
"I'm very pleased with Nathaniel (Mendez-Laing), he started to get people on their feet when he got the ball and I think it shows he has the ability to run at people and create things for us.
"I think if we have the same attitude and get the same amount of balls and chances that we've had in our next game then we'll score."
Doncaster Rovers manager Dean Saunders told BBC Radio Sheffield:
"Another great win for us. We showed a lot of determination and the back four defended great.
"The goalkeeper had two shots straight at him and one over the bar.
"We should have killed them off, we had loads of chances in that second half but some of the football we played at times was excellent."