Stevie May grabbed an impressive hat-trick for Killie and United will be missing another player after Calum Butcher was dismissed in the 20th minute for a professional foul.
McNamara made eight changes after Thursday's 4-1 defeat by St Mirren, with Keith Watson suspended after another red card, and he shed some light on his selection problems after the game.
"Injuries were behind it," said the United boss. "A few of the boys were carrying knocks but I took a gamble by putting (Gary) Mackay-Steven and (Stuart) Armstrong on the bench after they passed a fitness test this morning.
"(Ryan) Gauld is out with a groin problem, Gavin Gunning is struggling with his knee and Keith Watson is obviously suspended after being sent off in the last game. So a lot of it was forced.
"The only one that wasn't forced was leaving out John Rankin for (Morgaro) Gomis. John has played a lot of games
"Putting Mackay-Steven and Armstrong on the bench was a gamble and hopefully they'll be okay for Wednesday. I don't know how many of the boys will be fit for the Aberdeen game, hopefully I'll have a better idea tomorrow."
Butcher had to make a desperate last-man challenge after a poor headed back pass from skipper Sean Dillon and McNamara was frustrated by his side's costly defensive lapse.
"The sending off killed us with that happening 15 minutes into the game and obviously them getting the opening goal from the penalty," he said.
"It was the turning point of the game and I'm disappointed with the concentration at that point. I said to the players before the game that the main threat from St Johnstone would be balls from the corners or over the top, so we had to be switched on."
St Johnstone boss Tommy Wright was glad that May ended his recent barren run, but insists all his players deserve credit for a convincing win.
He said: "I just hope the performance is not over looked by the fact they had a man sent off because even with 11 men, I don't think they would have been able to compete with us today, because I thought we were excellent.
"Stevie has had a good season and it was maybe a wee test for him today. He hadn't scored for a few weeks but he works hard and is always a threat. I'm really pleased that he got his hat-trick.
"Hopefully he can kick on again and go on a wee run again.
"I'm pleased with Stevie but just as I am with the rest of the lads. Stevie will get the headlines but it was an excellent team performance."