On-loan Leeds winger Ramon Nunez struck his third goal for Scunthorpe to give them a half-time lead, but David Nugent pounced to fire home an 81st-minute deflected equaliser for Pompey.
Preston's win over Watford lifted them above Sheffield United and Scunthorpe on goal difference and Knill, who replaced Ian Baraclough as Iron boss at the end of March, will waste no time in his bid to steer his side straight back to the npower Championship.
Knill said: "I'm hoping to be able to bring in five or six new faces during the summer. We've a number of players in mind who we would like to bring in, but there will also be interest from other clubs and it promises to be a difficult summer for us.
"The writing was on the wall as far as this season was concerned some time ago. All I asked of my players for this final game was to go out and give us a performance.
"I think we did that, but once again we were let down with what happened in the two penalty boxes. Ramon Nunez scored an excellent goal for us and we had some other good chances, but could not put them away."
Source: PA
Source: PA