Ronaldo, hoping to end Messi's three-year run as World Player of the Year, thrilled the Bernabeu when he snatched a 90th-minute winner in Real Madrid's 3-2 victory over Manchester City in Group D on Tuesday.
Messi not only netted Barca's 71st-minute equaliser against the unfancied Russians at the Nou Camp, but also grabbed the winner with a rare header 10 minutes from time.
The Argentina international has been top scorer in Europe's elite club competition the past four seasons and his latest double took his Champions League goal tally to 53 in 69 appearances while Ronaldo has 39 in 81 matches.
"We deserved to win but it was a really tough game," Messi told Spanish television.
"It's not easy when they defend so deep and you can't find the spaces," added the 25-year-old, who has now scored 109 goals in his last 100 official matches for Barca.
"They were comfortable defending in their penalty area and they have very strong and quick forwards and can break quickly.
"Things got complicated but we kept pressing and we managed to turn it around."
The match had appeared to be going Barca's way when B team youngster Cristian Tello struck to make it 1-0 in the 14th minute but Spartak were level a quarter of an hour later when Daniel Alves turned the ball into his own net.
The visitors' ultra-defensive tactics frustrated Barca and they were flirting with a first home defeat in 17 European outings since falling 2-1 to another Russian side, Rubin Kazan, in October 2009.
Barca's fightback ensured Spartak's Spanish coach Unai Emery, a former boss at La Liga sides Almeria and Valencia, is still seeking his first win against Barca after 13 attempts.
"I have had the poor luck never to have beaten Barca but every time I come here I try to win," Emery told a news conference. "It's not impossible and it's be
