The defeat was Tottenham's second in a row and third in their last five outings.
The North London outfit were missing the services of Pierre-Emile Hojbjerg, Cristian Romero, Richarlison and Dejan Kulusevski due to injuries and Conte pointed to the quartet's absence as a major contributor to their defeat.
Harry Kane's tenth Premier League goal of the season was only enough to be considered as a consolation after Callum Wilson and Miguel Almiron established a two-goal lead for the visitors.
Conte charged Spurs fans to look at the bigger picture in his post-match reaction, with his side holding onto third place for now.
Asked about the half-time jeers, Conte told Sky Sports: "The fans need to understand, we are doing our best in every moment, and also [against Newcastle] the commitment was really high.
"For sure, in this moment we have to face a difficult moment for us because when you don't have three or four players in the squad, you are in trouble.
"We have to manage this situation and overcome it together. Without four players, this squad doesn't have the [depth] to lose four players at the moment.
"I always said before starting this second path [season], the important teams, the teams who will fight for the title, you'll see the team during this period when you play every three days. You need to have a deep squad, a strong squad with great quality.
"I think we have only just started our process last season. From [Europa] Conference League, we are now playing in the Champions League."
"We're trying to improve our situation step by step, but you need time and patience," he continued. "These must be very clear for everybody.
"I want to be honest. With my experience, I continue to tell we are doing well – it's a bad situation but we need the time and patience, and to have these kinds of problems in order to understand how to overcome them in the future.
"If we played one game every six or seven days, I think we could fight for something important. To play every three days, I think we have to continue to build our path and have patience, don't be disappointed too much because, I repeat, if someone thinks we can invent the win and do a miracle… We need to continue to work.
"You have to understand we are in a process, and we have just started the process. If someone doesn't want to listen, it's not my problem."
