Morata made his case to start Sunday's World Cup qualifier away to Macedonia with a towering header.
After Edwin Cardona had cancelled out David Silva's opener for the hosts, Radamel Falcao's first international goal for two years had Colombia on course for a famous win.
However, Morata made his case to start Sunday's World Cup qualifier away to Macedonia with a towering header three minutes from time to save Spain's blushes.
"I always want to play for Spain," Morata, who joined up with the squad earlier than scheduled after helping Real Madrid retain the Champions League against his old side Juventus on Saturday, told Telecinco.
"We had them on the ropes at the end and (the win) escaped us, but it is a good sign because this a game that could easily be the quarter or semi-finals of a World Cup."
Lopetegui ran the risk of an adverse result as Nacho was the only Real player to start, whilst David de Gea, Sergio Busquets and Diego Costa were also left on the bench.
Colombia boss Jose Pekerman gave James Rodriguez and Juan Cuadrado the chance to bounce back from their Champions League final disappointment -- Rodriguez was left out of the Real squad, whilst Juventus's Cuadrado was sent-off just 17 minutes after coming on as a substitute.
Cuadrado had the first serious effort on goal as his long-range shot was spilled by Pepe Reina on a night to forget for the Napoli goalkeeper, but Falcao was flagged offside as he attempted to mop up the rebound.
Spain went ahead with characteristic panache on 22 minutes when Silva finished off a brilliant team move to score his seventh international goal in Lopetegui's short reign.
Iago Aspas freed Pedro Rodriguez down the right and his low cross was turned home by Silva despite the best efforts of Arsenal goalkeeper David Ospina.
Rodriguez looks set to leave Madrid this summer, but the top scorer at the 2014 World Cup gave a glimpse of his quality with a lovely turn and shot with the outside of his left foot that curled just wide.
Colombia were gifted a route back into the game when their equaliser arrived five minutes before half-time, though, as a mix-up between Reina and Cesar Azpilicueta allowed Cardona to loop into an unguarded net.
Lopetegui replaced the experience of Silva and Andres Iniesta with Saul Niguez and Marco Asensio at the break, both of whom who will take their places in Spain's under-21 squad for the European Championships later this month in Poland.
And they should have combined to put Spain back in front but Asensio's poor cross was intercepted by Ospina with Niguez waiting for a tap in.
Falcao looked to have inflicted a rare home defeat on Spain when he powered home Rodriguez's corner 10 minutes into the second-half.
However, Morata, another player heavily linked with a move away from the Santiago Bernabeu in the coming weeks, extended Lopetegui's unbeaten run to nine games in charge with a brilliant header to turn Niguez's cross into the far corner.