The Hammers won 1-0 at St Mary's on Thursday to lie 13th in the table - nine points clear of the relegation zone.
Goalkeeper Lukasz Fabianski, centre-back Max Kilman and midfielder Carlos Soler were forced off against Southampton due to injuries, while Tomas Soucek and Guido Rodriguez received bookings that triggered one-match suspensions.
"Always we are happy when we achieve one victory," Lopetegui said. "Now we have to manage and to handle these problems for the next big challenge against Liverpool."
Alphonse Areola performed well in goal against the Saints in place of Fabianski, who took a nasty blow to the face in the 29th minute.
Jean-Clair Todibo, meanwhile, impressed after he replaced Kilman.
"The players on the bench show they were ready, which is good news because you know how you are going to start one match but you don't know what is going to happen, so you have to be ready to be competitive," said Hammers manager Lopetegui.