Due to injuries, loans and a first team call up for skipper Callum Ward, only four second year scholars were in the line up which also included a first start for U16 Tinashe Chavundura and a change of formation for the young Imps.
Rotherham started the brighter, penning Lincoln in their own half and the visitors took the lead after 15 minutes when an early cross was volleyed past Henry Smith in the Imps goal.
But the Imps levelled just one minute later as Jordan Harper ran onto a pass behind the visitors' back four, the keeper dived at his feet and the ball ricocheted into Harper's path and he slotted the ball home from close range.
The Imps began to take charge and good play from Matt Bowles found Kegan Everington who powered a left foot strike into the top corner from 25 yards.
Goalkeeper Smith pulled off a fantastic reaction save to keep the Imps in front and moments before half-time Lincoln extended their lead when a corner by Bowles was headed up in the air by a Rotherham defender and Nick Green reacted quickest to head home.
Rotherham gained the early momentum in the second half and they rediced the deficit when a midfielder was released behind the back four and he slotted it past Smith. Under 16 Liam Harris replaced Chavundura on the hour, and the Imps regained a two goal lead when hard work from Josh Barr-Rostron, who had an excellent game in midfield, got him behind the full back and he squared the ball to Kieran Helsdown who slotted the ball between the keeper's legs and into the bottom corner.
The visitors had their share of possession but the back four of Green, Jordon Cooke, Kieran Walker and Mason Love stood firm.
The Imps showed tremendous resilience and managed the remainder of the game very well, and the hard-working performance was rewarded with a solid victory against a strong Rotherham side, and a four-game unbeaten run to round off the year.
Team: Smith, Love, Walker, Everington, Cooke, Green, Barr-Rostron, Bowles, Harper, Helsdown, Chavundura. Subs: Lilley, Harris, Stewart, Scott.