Smith’s goals dried up at the back end of last year as he went seven games without bagging after a prolific start to the season.
Smith opened the scoring five minutes before the break when he powered home Shane Ferguson’s cross at the far post.
But with three sides of the AESSEAL New York Stadium still celebrating, Bolton hit straight back as Eoin Doyle fired home in clinical fashion.
Smith made a long spell of second-half pressure count as he sent another header into the corner to take his tally to 17 goals for the season.
The 30-year-old is out of contract at the end of the season and the Millers will hope that his return to the goals, which coincides with the January transfer window opening does not spell trouble for them.
Smith’s brace ending up settling matters, but only because Bolton missed two chances at the death to snatch a point.
The win sees the Millers return to the summit of the table, after Sunderland had knocked them off in midweek, and they got back to winning ways after their Boxing Day defeat at Accrington.
Warne said of Smith: “He took his two goals really well today, he's played better, he's played a lot worse.
“I think it was a decent seven out of 10 for Smudge. It wasn't that amazing, I mean massive surprise he got man of the match - give it to the person who scores not to anyone else!
“He was good and he's always a threat and as I always say about Smudge, his work rate right around the box, sometimes he's the one who crosses it.
“Great for Smudge to get two goals, great to win again. I would prefer it was 3-1 and I could enjoy the last few minutes but that's not how football is it's theatre, it's entertainment and hopefully everyone stayed for the final whistle and enjoyed the last few minutes of torture.”