Substitute Munir El Haddadi averted a first home defeat for Barca in more than two years by sliding in an equaliser in the 84th minute, meeting a cross by Messi who had been sent on along with Busquets in the second half as Barca chased the game.
Philippe Coutinho gave the champions the lead in the 12th minute with a classy volley and Lionel Messi smacked a shot against the bar as Barca, resting Jordi Alba and Luis Suarez, made a strong start against Leganes, who began the game bottom of the table.
In between, Umtiti was already missing Wednesday's Champions League game against Tottenham through suspension.
"We thought that this was the moment to rest Messi", said the manager's number two Jon Aspiazu.
"When I make the decision, I think about what's best for my team and for my club", he said to reporters after the match.
In the end, Leganes hung on to claim three points and handed Barca their first defeat of the season.
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A World Vision New Zealand spokesperson, Tilly Redstone, said all its people in Indonesia had been accounted for and were okay. Indonesian TV showed a smartphone video of a powerful wave hitting Palu , with people screaming and running in fear.
Leganes' victor came thanks to a blunder by veteran central defender, Gerard Pique, who misplayed a shot while trying to clear the ball from inside the area.
Busquets replaced the injured Sergi Roberto early in the second half. We didn't create the chances we'd have liked.
Leganes had to wait until the 30th minute for their first opening as Youssef En-Neysri broke into the box and picked out Rubén Pérez, who fired straight at goalkeeper Marc-Andre Ter Stegen.
Messi's arrival brought added impetus from the home side and once again he went close, hitting the post 13 minutes from time.
"He is the best in the world but we can't rely on Leo to always sort everything out for us", Suarez said.
"If we do well as a team, not just as individuals, we can pen Barcelona back, not just Messi".
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