Rangers were agonisingly beaten on penalties by Eintracht Frankfurt after the teams were deadlocked at 1-1 at the end of extra-time in Seville.
Joe Aribo fired Rangers in front just before the hour mark before Rafael Borre levelled up for the Germans 12 minutes later.
In the tense penalty shootout, Ramsey - brought on in the 117th minute - was the only player to miss from the spot, leading to criticism of the Welshman and his loan spell in Glasgow.
But McCoist was surprised to see the former Arsenal man used sparingly on the night, having seemingly proven his fitness by playing 60 minutes in Saturday's 3-1 Scottish Premiership win over Hearts.
"I was surprised," McCoist said of Ramsey's omission. "We don't know the real fitness situation, we don't know how fit these guys are but he played at the weekend.
"I was probably more surprised there was no Kemar Roofe," McCoist added about the frontman, who was passed fit for the bench after a spell on the sidelines.
"Joe Aribo has done reasonably well in that position [striker]. However, if you're playing a centre forward [referring to Roofe] who knows the position, plays the position, that was the one that probably surprised me more."
McCoist felt that Rangers looked more dangerous as the game wore on but rued Ryan Kent's big chance to win the game in the dying moments of extra-time.
The former Gers striker said: "I thought they started better than us and to be honest with you, I thought we finished better than them. I thought as extra time went on, we were stronger.
"And obviously with the big chance with a couple of minutes to go, that was the one where Roofe came on, cut it across and Kent, if anything, meets it too well and the keeper makes a great save."
Eintracht kept their nerve to convert all five of their penalty kicks and the Ibrox legend was full of praise for the quality on display in the shootout.
"I don't think I've seen in any penalty competition, five better penalties,2 he said.
"Believe it or not, you fancy [Rangers goalkeeper, Allan] McGregor at penalties, he's a brilliant goalkeeper but you've got no chance; unsavable. They flew into the top corner and bottom corner."
Rangers defender Calvin Bassey has come in for rave reviews following his performance in Seville and McCoist believes the 22-year-old could walk into any team based on his final heroics.
"What about that performance, he was absolutely frightening, he's walking in anywhere on that performance." he added.
Rangers manager must somehow lift his dejected squad ahead of this weekend's Scottish Cup final against Hearts, which presents the club's final opportunity of landing silverware this season after surrendering the league title to Old Firm rivals Celtic.