The skipper made his first start in more than a month in the South London clash due to Darnell Fisher having a hip flexor injury.
Clarke made a big impact, heading North End’s second goal in the 3-1 victory.
PNE manager Neil felt the nature of the game was very much up Clarke’s street.
“Tom did what he always does, he came in at Millwall and was solid,” said Neil.
“If I had to pick a game for Tom to come back to play in, it would be Millwall away.
“Tom is a man, he goes and competes and fights.
“Millwall normally bump Murray Wallace up that side, kick to the right-back area and Ben Marshall drops in.
“They saw Tom there and chose not to do that, which was a good decision.
“We asked Tom to do a job and he did it well.”
Clarke’s last appearance had been in the 1-1 draw with Swansea on January 12.
He limped out of that game with a calf strain, returning to the bench on February 1 for the goalless draw against Derby County.
In his absence Fisher hit form in the right-back slot, with Jordan Storey and Ben Davies cementing a strong partnership in the middle.
So 31-year-old Clarke had to show a lot of patience before getting his chance at The Den.
Clarke’s goal saw him on the scoresheet for the first time since December 2017 when he scored a late winner against Cardiff.
He is still wearing a mask to protect his nose which he broke in a clash of heads with his former team-mate Jordan Hugill in November.
The injury for Fisher is not thought to be a long-term one, with the right-back travelling to Millwall with the squad and watching the game from the stand.
Neil said: “Darnell’s hip flexor wasn’t quite right for the game.
“We will see how he is over the next few days and go from there.”
The enforced change at right-back did mean a first inclusion in the squad for Joe Rafferty at Millwall – he was an unused substitute.
Rafferty joined in January from Rochdale but Fisher’s good form and the good shape of the squad meant a wait on the sidelines.
He has played in a couple of training ground friendly games to maintain his match sharpness.
The Preston squad were back in training today, Neil having granted them Sunday and Monday off.
His focus is on the build-up to Saturday’s Deepdale clash with Bristol City, the Robins in that pack of clubs just ahead of 10th place North End in the table.