Guardiola watched his side extend their 100 per cent start to go top of the Premier League from Barcelona, where he is recovering from back surgery.
City turned in a dominant display at a sold-out Bramall Lane, but went close to letting two points slip when Blades substitute Jayden Bogle fired an 85th-minute equaliser.
When asked if he enjoyed taking charge in Guardiola’s absence, Lillo said: “Not at all. I much prefer being with Pep. Especially when it’s a question of health, I don’t enjoy this at all. We miss his presence now more than ever.
“I haven’t spoken to him after the match. During the match I spoke to him at some moments, but generally he was speaking to the other members of the technical staff. But he’s been totally present today.”
City dominated possession throughout and were rarely troubled by the Blades, who produced a resolute and disciplined defensive display.
Haaland steered his 37th-minute penalty on to a post after Blades skipper John Egan had handled, but made amends by heading his side in front in the 63rd minute.
“Generally I thought we played really well today,” said Lillo, who confirmed Phil Foden had started on the bench due to an upset stomach. “It was a lot closer to what we wanted.
“From the second half I thought we really found our rhythm and we were able to win the ball back a lot quicker.
“We were able to find the new spaces created from winning the ball back quicker and we could have scored more before the first goal went in.”
Blades boss Paul Heckingbottom feels his side, back in the top flight after a two-year absence, are also improving despite losing their first three matches.
Heckingbottom said: “I’m pleased with the performance. You need a perfect performance to beat them because that wasn’t a below-par City.
“We got punished for two things we should do better. The sickener for me is the nature of how Rodri has lashed it in.
“It just comes after Phil (Foden) has mis-controlled the ball and just drops into his path.
“It’s a kick in the teeth after all the good play they had had and they way we had dealt with it. We’ve lost a point, but we’ll focus on the performance I think.
“Game on game we’ve got better and we certainly believe we’re going to have enough.”