Jon-Paul McGovern nearly put Carlisle ahead after 23 minutes, his stunning 25-yard free-kick wrong-footing Pompey goalkeeper Simon Eastwood and crashing off a post. The ball then hit Eastwood and almost deflected back into the net but he somehow scrambled it to safety.
Carlisle's Liam Noble came close three minutes after the break but a superb volley from the edge of the box was palmed away by Eastwood.
He was unable to deny Rory Loy the opener, though, after 51 minutes. The Carlisle number nine raced on to a stunning throughball from skipper Lee Miller, rounded Eastwood and slotted home coolly.
But Pompey, who ended a nine-game losing streak with a 0-0 draw at Hartlepool on Tuesday, levelled the scores after 78 minutes.
Substitute John Akinde tripped as he tried to round Carlisle 'keeper Mark Gillespie. Referee Carl Berry rightly opted against sending Gillespie off, but Walker sent him the wrong way with the resulting penalty - although Pompey still dropped to the bottom of League One following Hartlepool's late success.