But the Spain striker hobbled off in the 35th minute against City at Stamford Bridge, holding his left hamstring.
"It's a muscular problem," Conte told reporters after Kevin De Bruyne's excellent 67th-minute goal sent Pep Guardiola's side back to the top of the Premier League table.
"I don't think it's a serious problem because he stopped before it will become a serious injury.
"He said to me, 'Coach, I prefer to stop myself otherwise I risk a bad injury'. I don't know.
"The doctor now in the next days has to check the situation, but I don't think he's available for the national team.
"It's normal when you play three massive games in only seven days, you must consider this aspect [fatigue].
"We needed to take this risk because Morata for us is an important player."
Conte's reliance upon Morata as the leader of his attack was underlined when winger Willian came on in his place, with Belgium striker Michy Batshuayi held back until his compatriot De Bruyne broke the deadlock to give the visitors the lead.
"It was a simple tactical decision," the Italian said.
8 - Chelsea have dropped eight points in four Premier League home games so far in 2017-18; two more than in the whole of 2016-17 (6). Gloom. pic.twitter.com/gokdpS8Aiu— OptaJoe (@OptaJoe) September 30, 2017
"In this type of game I thought Willian with [Eden] Hazard was a good decision, to try to exploit the space behind the defenders. It's a simple tactical decision."
Chelsea are now six points off the pace set by the Manchester clubs at the summit – United are one shy of City on goal difference after thumping Crystal Palace 4-0 – but Conte pointed towards a tough run of fixtures handed to his side over the opening weeks of the season.
"I think our start wasn't so, so easy. I think we have the points that we deserve."
On City's title credentials, Conte added: "Last season Manchester City was a very good team, very strong.
"I think after this transfer market they improved a lot. They strengthened, I think so.
"It's right to compliment our opponent. This is football. We have to accept the result, above all because we know that we gave everything."