Eric Kinder's young side put in a much improved display as they ran the title chasers close in Cobham.
The Under-21s coach had named his youngest side of the season, with all but three of the starting eleven eligible to play for the Under-18s, and that lead to a hesitant start from Rovers as they looked to contain their hosts.
Chelsea, unbeaten since September in the league, forced the pace from the off, but clear-cut chances were at a premium in the opening exchanges, Scottish Under-21 international Islam Feruz forcing Rovers keeper David Raya into a save.
The Spaniard then denied Lewis Baker, but on 25 minutes the deadlock was broken, Feruz beating the Rovers offisde trap to race through and finish well.
Rovers had their backs to the wall after that as Chelsea went looking for more goals, Nathan Ake, John Swift and Lewis Baker all spurning chances as it ended 1-0 at the break.
The second half saw Rovers come out with renewed enthusiasm and they were more than a match for their high-flying opponents.
Luke Wall, the 17-year-old striker making his first start, had a great opportunity to open his account, but he couldn't test Jamal Blackman at the back post, eventually seeing his effort blocked.
With Chelsea contained Rovers pressed for an equaliser, but they too struggled to create meaningful openings, Devarn Green putting a free-kick narrowly over, whilst at the other end Chelsea substitute Adam Nditi was denied.
Kinder's side never gave up and continued with their attacking play deep into injury time but they couldn't grab that elusive goal to send them back to the north west with a share of the points.
"The lads worked their socks off, they put in a great effort," said Kinder.
"We were a young side against one of the most highly-rated and experienced squads in Under-21 football.
"It was great experience for them and should serve them well in the advancement of their careers."
ROVERS: Raya, Fernandez, Bauress, Tanner, Lavelle, Lenihan (c), Green, Doyle, Rittenberg (sub Pero 72 mins), Beesley, Wall (sub Paul 72 mins).
Subs not used: Paulo Jorge, Williams (GK), Cotton.