Nahki Wells opened the scoring and Luke Prosser put through his own net to make it 2-0, but the Shrimpers hit back through Ryan Cresswell and Gavin Tomlin.
Parkinson said: "The players have come here and put their bodies on the line again for this football club and there really is so much I can ask of them.
"They been fantastic and did well again for most of this match.
"Unfortunately, Southend came back to get a point and it's disappointing to concede right at the end.
"But we've played well and just couldn't quite see the job through.
"I thought Southend's first goal was questionable as our keeper was fouled but there are a few tired legs in a dressing room and I will be resting a few of them for the cup replay against Brentford next week."
- Sports & Recreation
- Ryan Cresswell
- Luke Prosser