Vieira’s team still sputters and clunks occasionally on defense — on set pieces in particular, and as it did by yielding both goals during the final 10 minutes in Toronto. (N.Y.C.F.C. gave up 57 goals in 34 matches this season, just one fewer than it allowed in 2015, when the club finished eighth.) Still, after watching the game film from last weekend three times, Vieira stood by each of his decisions against Toronto, and he refused to place a disproportionate share of the blame on his frequently leaky back line.

“When we talk about goals, we always talk about the personnel in the back, but that’s not the problem,” he said. “The problem is the collective, the protection for the back four, the work from the people up front. We score a lot of goals by building up from the back, creating more space for the strikers. For the defending side, if we do our work in front of the back four, it would be more easy for them.

“As a team, we didn’t defend well. We have to improve for next year.”

For now, Vieira is still concerned with this year, and with figuring out his lineup for Sunday based on experience, health and form. His decisions in the first leg were surprising. He started goalkeeper Eirik Johansen over the veteran Josh Saunders, who had played in 33 games. Despite electing to rest midfielder Andrea Pirlo (calf), he chose not to start Lampard, who insisted he had been “raring to go” for more than a week after a recent injury of his own. Vieira also removed Villa in the 78th minute while the game was scoreless.

A published report Monday said “livid” players had held a gripe session over Vieira’s decisions, but players and team officials vehemently denied such an event had taken place. “It’s nonsense, been made up,” Lampard said. “Any discord is because we lost.”

Lampard, however, did hint that he would like to see the team’s three highest-paid stars — himself, Pirlo and Villa — back on the field together Sunday. “In big games, big players more often than not will make the difference,” he said.

And even as a first-year coach, Vieira is smart enough to understand how his celebrated stars might find it hard to accept a lesser role. He, too, carried a celebrated, championship-winning résumé to the final stops of his playing days. He recalled being benched by José Mourinho at Inter Milan and by Roberto Mancini at Manchester City near the end of his career.