The result was enough to keep Barcelona in the lead after Real Madrid and Atletico Madrid went 0-0 in the derby.
"I have to judge the games we have coming up and we have four games in the space of 10 days, I have to think about what might happen and I thought Leo and Busquets had to rest, knowing that we have a very tough game on Wednesday and we have a large squad", Valverde said.
Messi also stated, "You are threatening me, you are threatening me".
"When I make the decision, I think about what's best for my team and for my club", Valverde was quoted as saying by FootballEspana.
That was famously Barca's only defeat last season as they narrowly missed out on their own "invincible" campaign, but what is even more incredible is that Messi's run still falls some way short of the record unbeaten streak in LaLiga, which is held by another Barcelona legend.
Busquets replaced the injured Sergi Roberto early in the second half.
Leganes, however, will draw positives from the match as they will hoping to get out of the bottom three on the La Liga table.
Brazil superstar Philippe Coutinho opened scoring for the Catalans in the 12th minute of the encounter after being assisted by Lionel Messi.
Marc Andre Ter Stegen has been poor since the start of this season and shipped in two more goals against the Cucumber Growers from Madrid.
Oscar De Marcos gave Athletic a first-half lead but Messi came on after the interval to rescue his side a point by setting up fellow substitute Munir El Haddadi. We didn't create the chances we'd have liked.
Barca continued to push for a second goal and were almost rewarded in the 16th minute when Lionel Messi rattled the crossbar with a strike from the edge of the box.
Barca striker Suarez was critical of his side's performance and their continued dependence on Messi.
"We can't depend on Messi to enter the match and solve things for us", Suarez said.