Willian’s fine strike just after the hour mark had put Chelsea in command after earlier hitting both posts in the first half.
However, one moment of carelessness cost Chelsea dear as Andres Iniesta intercepted Andreas Christensen’s pass to tee up Messi to swing the balance of the tie in Barca’s favour 15 minutes from time.
The English champions must now score when they travel to the Camp Nou on March 14 to have any chance of making the last eight.
Chelsea manager Antonio Conte sprang a surprise before kick-off by leaving out both Olivier Giroud and Alvaro Morata with Eden Hazard instead operating in the middle of a front three featuring Willian and former Barca winger Pedro Rodriguez.
And it was Hazard who sent the first warning that Barca were in for an uncomfortable evening when he fired just over from 20 yards five minutes in.
Antonio Rudiger also headed just wide in a positive opening from the hosts, but it was Barca who had the first clear chance on 16 minutes.
Chelsea constantly tried to surround Messi with three or four blue shirts to limit the Argentine’s threat, but he dug out a cross to the far post where an unmarked Paulinho headed wide.
Barca then went on to dominate possession for a large spell of the first half with their control of the ball reaching 80 percent at one stage.
However, the visitors lacked penetration before the break and were lucky to go in level at half-time.
Willian showed his ability to score from outside the box off either foot with a double against Hull City to take Chelsea into the FA Cup quarter-finals on Friday.
He was inches away from another long-range stunner when he curled onto the post from 25 yards with Marc-Andre ter Stegen beaten in the Barca goal.
Barca had kept six clean sheets in their previous seven Champions League games, but once again had good luck rather than good defending to thank four minutes before the break when Willian hooked another effort from outside the box off the woodwork.
Hazard then volleyed just over as Chelsea ended the half on a high.
Barca appeared to have restored order early second period, but failed to learn their lesson of Willian’s danger from the edge of the box.
A short corner was worked into the Brazilian’s path and he arrowed a low shot past the rooted Ter Stegen.
However, Barca remain unbeaten in 31 La Liga and Champions League games under Ernesto Valverde thanks to a late rally.
Luis Suarez had claims for a penalty waved away when he went down under pressure from Rudiger.
But Barca’s protests had barely been silenced before they were level.
Christensen’s dangerous ball across his own box was a gift for an old scourge of Chelsea in Iniesta.
At the end where he broke Chelsea hearts with a stoppage-time equaliser in a highly controversial semi-final in 2009, Iniesta this time squared for Messi to apply the finishing touch low past Thibaut Courtois for his 28th goal of the season.