Capaldi missed last week's games becuase his wife had just had a baby and Kennedy had only just signed and was not ready to play.
"Setubal will provide a tough test and that's what we want," Jones told the Western Mail. "We played them in Portugal last season and it will be difficult again.
"We are running at maybe 80 per cent right now and that's exactly where we want to be. Pre-season is all about preparation.
"The players have come back lean and fit. Now they need time on a football pitch, getting used to the full size.
"You cannot recreate that in training - and they will have another taste of that against Vitoria Setubal.
"The key word is preparation. It's no good being flat out now and then hitting a dull patch when the league matches start. By the time we go into our pre-season home match against Ajax we want everybody at full pelt and 100 per cent ready for the new campaign."
Today's game is near Lisbon and is meant to be a behind closed doors training match. The serious action kicks off on Tuesday when City face Guimaraes in the Algarve Challenge Cup in Faro (7:15pm). The same night Middlesbrough play Celtic in the same stadium.
Then it's a reversal of fixtures with Cardiff playing Celtic to end the competition after 'boro play Guimaraes. City and Middlesborough do not play each other.
The game with Celtic is live on Setanta Sports for those who have not made the trip to Portugal. It's kicks off at 9:30pm.
City then have two more senior friendlies. Away at Swindon on Tuesday July 29th and then at home to Ajax on Friday August 1st.
The Championship kicks off with a home game against Southampton on August 9th, ko 3:00pm.